gnu/packages/maths.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
   3 ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
   4 ;;; Copyright © 2014 John Darrington <jmd@gnu.org>
   5 ;;; Copyright © 2014 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 Ricardo Wurmus <rekado@elephly.net>
   9 ;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
  10 ;;;
  11 ;;; This file is part of GNU Guix.
  12 ;;;
  13 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  14 ;;; under the terms of the GNU General Public License as published by
  15 ;;; the Free Software Foundation; either version 3 of the License, or (at
  16 ;;; your option) any later version.
  17 ;;;
  18 ;;; GNU Guix is distributed in the hope that it will be useful, but
  19 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  20 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  21 ;;; GNU General Public License for more details.
  22 ;;;
  23 ;;; You should have received a copy of the GNU General Public License
  24 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  25
  26 (define-module (gnu packages maths)
  27   #:use-module (ice-9 regex)
  28   #:use-module (gnu packages)
  29   #:use-module ((guix licenses) #:prefix license:)
  30   #:use-module (guix packages)
  31   #:use-module (guix download)
  32   #:use-module (guix svn-download)
  33   #:use-module (guix utils)
  34   #:use-module (guix build-system cmake)
  35   #:use-module (guix build-system gnu)
  36   #:use-module (gnu packages algebra)
  37   #:use-module (gnu packages bison)
  38   #:use-module (gnu packages check)
  39   #:use-module (gnu packages cmake)
  40   #:use-module (gnu packages compression)
  41   #:use-module (gnu packages curl)
  42   #:use-module (gnu packages elf)
  43   #:use-module (gnu packages flex)
  44   #:use-module (gnu packages fltk)
  45   #:use-module (gnu packages fontutils)
  46   #:use-module (gnu packages gettext)
  47   #:use-module (gnu packages gcc)
  48   #:use-module (gnu packages gd)
  49   #:use-module (gnu packages ghostscript)
  50   #:use-module (gnu packages glib)
  51   #:use-module (gnu packages gtk)
  52   #:use-module (gnu packages less)
  53   #:use-module (gnu packages lisp)
  54   #:use-module (gnu packages gnome)
  55   #:use-module (gnu packages xorg)
  56   #:use-module (gnu packages gl)
  57   #:use-module (gnu packages m4)
  58   #:use-module (gnu packages mpi)
  59   #:use-module (gnu packages multiprecision)
  60   #:use-module (gnu packages pcre)
  61   #:use-module (gnu packages popt)
  62   #:use-module (gnu packages perl)
  63   #:use-module (gnu packages pkg-config)
  64   #:use-module (gnu packages python)
  65   #:use-module (gnu packages readline)
  66   #:use-module (gnu packages tbb)
  67   #:use-module (gnu packages tcsh)
  68   #:use-module (gnu packages tcl)
  69   #:use-module (gnu packages texinfo)
  70   #:use-module (gnu packages texlive)
  71   #:use-module (gnu packages xml)
  72   #:use-module (gnu packages zip))
  73
  74 (define-public units
  75   (package
  76    (name "units")
  77    (version "2.11")
  78    (source (origin
  79             (method url-fetch)
  80             (uri (string-append "mirror://gnu/units/units-" version
  81                                 ".tar.gz"))
  82             (sha256 (base32
  83                      "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
  84    (build-system gnu-build-system)
  85    (synopsis "Conversion between thousands of scales")
  86    (description
  87     "GNU Units converts numeric quantities between units of measure.  It
  88 can handle scale changes through adaptive usage of standard scale prefixes
  89 (micro-, kilo-, etc.).  It can also handle nonlinear conversions such as
  90 Fahrenheit to Celsius.  Its interpreter is powerful enough to be used
  91 effectively as a scientific calculator.")
  92    (license license:gpl3+)
  93    (home-page "http://www.gnu.org/software/units/")))
  94
  95 (define-public double-conversion
  96   (package
  97     (name "double-conversion")
  98     (version "1.1.5")
  99     (source (origin
 100               (method url-fetch)
 101               (uri (string-append
 102                     "https://github.com/floitsch/double-conversion/archive/v"
 103                     version ".tar.gz"))
 104               (file-name (string-append name "-" version ".tar.gz"))
 105               (sha256
 106                (base32
 107                 "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
 108     (build-system cmake-build-system)
 109     (arguments
 110      '(#:test-target "test"
 111        #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
 112                            "-DBUILD_TESTING=ON")))
 113     (home-page "https://github.com/floitsch/double-conversion")
 114     (synopsis "Conversion routines for IEEE doubles")
 115     (description
 116      "The double-conversion library provides binary-decimal and decimal-binary
 117 routines for IEEE doubles.  The library consists of efficient conversion
 118 routines that have been extracted from the V8 JavaScript engine.")
 119     (license license:bsd-3)))
 120
 121 (define-public dionysus
 122   (package
 123     (name "dionysus")
 124     (version "1.3.0")
 125     (source (origin
 126               (method url-fetch)
 127               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
 128                                   ".tar.gz"))
 129               (sha256
 130                (base32
 131                 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
 132     (build-system gnu-build-system)
 133     (inputs `(("tcl" ,tcl)))                      ;for 'tclsh'
 134     (synopsis "Local search for universal constants and scientific values")
 135     (description
 136      "GNU Dionysus is a convenient system for quickly retrieving the values of
 137 mathematical constants used in science and engineering.  Values can be
 138 searched using a simple command-line tool, choosing from three databases:
 139 universal constants, atomic numbers, and constants related to
 140 semiconductors.")
 141     (license license:gpl3+)
 142     (home-page "http://www.gnu.org/software/dionysus/")))
 143
 144 (define-public gsl
 145   (package
 146     (name "gsl")
 147     (version "1.16")
 148     (source
 149      (origin
 150       (method url-fetch)
 151       (uri (string-append "mirror://gnu/gsl/gsl-"
 152                           version ".tar.gz"))
 153       (sha256
 154        (base32
 155         "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
 156     (build-system gnu-build-system)
 157     (arguments
 158      `(#:parallel-tests? #f
 159        #:phases
 160         (alist-replace
 161          'configure
 162          (lambda* (#:key target system outputs #:allow-other-keys #:rest args)
 163            (let ((configure (assoc-ref %standard-phases 'configure)))
 164              ;; disable numerically unstable test on i686, see thread at
 165              ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
 166              (if (string=? (or target system) "i686-linux")
 167                  (substitute* "ode-initval2/Makefile.in"
 168                    (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
 169              (apply configure args)))
 170          %standard-phases)))
 171     (home-page "http://www.gnu.org/software/gsl/")
 172     (synopsis "Numerical library for C and C++")
 173     (description
 174      "The GNU Scientific Library is a library for numerical analysis in C
 175 and C++.  It includes a wide range of mathematical routines, with over 1000
 176 functions in total.  Subject areas covered by the library include:
 177 differential equations, linear algebra, Fast Fourier Transforms and random
 178 numbers.")
 179     (license license:gpl3+)))
 180
 181 (define-public glpk
 182   (package
 183     (name "glpk")
 184     (version "4.55")
 185     (source
 186      (origin
 187       (method url-fetch)
 188       (uri (string-append "mirror://gnu/glpk/glpk-"
 189                           version ".tar.gz"))
 190       (sha256
 191        (base32
 192         "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
 193     (build-system gnu-build-system)
 194     (inputs
 195      `(("gmp" ,gmp)))
 196     (arguments
 197      `(#:configure-flags '("--with-gmp")))
 198     (home-page "http://www.gnu.org/software/glpk/")
 199     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 200     (description
 201      "GLPK is a C library for solving large-scale linear programming (LP),
 202 mixed integer programming (MIP), and other related problems.  It supports the
 203 GNU MathProg modeling language, a subset of the AMPL language, and features a
 204 translator for the language.  In addition to the C library, a stand-alone
 205 LP/MIP solver is included in the package.")
 206     (license license:gpl3+)))
 207
 208 (define-public pspp
 209   (package
 210     (name "pspp")
 211     (version "0.8.4")
 212     (source
 213      (origin
 214       (method url-fetch)
 215       (uri (string-append "mirror://gnu/pspp/pspp-"
 216                           version ".tar.gz"))
 217       (sha256
 218        (base32
 219         "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
 220     (build-system gnu-build-system)
 221     (inputs
 222      `(("cairo" ,cairo)
 223        ("fontconfig" ,fontconfig)
 224        ("gettext" ,gnu-gettext)
 225        ("gsl" ,gsl)
 226        ("libxml2" ,libxml2)
 227        ("pango" ,pango)
 228        ("readline" ,readline)
 229        ("gtk" ,gtk+-2)
 230        ("gtksourceview" ,gtksourceview)
 231        ("zlib" ,zlib)))
 232     (native-inputs
 233      `(("glib" ,glib "bin")             ;for glib-genmarshal
 234        ("perl" ,perl)
 235        ("pkg-config" ,pkg-config)))
 236     (home-page "http://www.gnu.org/software/pspp/")
 237     (synopsis "Statistical analysis")
 238     (description
 239      "GNU PSPP is a statistical analysis program.  It can perform
 240 descriptive statistics, T-tests, linear regression and non-parametric tests.
 241 It features both a graphical interface as well as command-line input.  PSPP
 242 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice.  Data
 243 can be imported from spreadsheets, text files and database sources and it can
 244 be output in text, PostScript, PDF or HTML.")
 245     (license license:gpl3+)))
 246
 247 (define-public arpack-ng
 248   (package
 249     (name "arpack-ng")
 250     (version "3.2.0")
 251     (source
 252      (origin
 253        (method url-fetch)
 254        (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
 255                            version ".tar.gz"))
 256        (file-name (string-append name "-" version ".tar.gz"))
 257        (sha256
 258         (base32
 259          "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
 260     (build-system gnu-build-system)
 261     (home-page "https://github.com/opencollab/arpack-ng")
 262     (inputs
 263      `(("lapack" ,lapack)
 264        ("fortran" ,gfortran-4.8)))
 265     (synopsis "Fortran subroutines for solving eigenvalue problems")
 266     (description
 267      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
 268 large scale eigenvalue problems.")
 269     (license (license:non-copyleft "file://COPYING"
 270                                 "See COPYING in the distribution."))))
 271
 272 (define-public lapack
 273   (package
 274     (name "lapack")
 275     (version "3.5.0")
 276     (source
 277      (origin
 278       (method url-fetch)
 279       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 280                           version ".tgz"))
 281       (sha256
 282        (base32
 283         "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
 284     (build-system cmake-build-system)
 285     (home-page "http://www.netlib.org/lapack/")
 286     (inputs `(("fortran" ,gfortran-4.8)
 287               ("python" ,python-2)))
 288     (arguments
 289      `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
 290        #:phases (alist-cons-before
 291                  'check 'patch-python
 292                  (lambda* (#:key inputs #:allow-other-keys)
 293                    (let ((python (assoc-ref inputs "python")))
 294                      (substitute* "lapack_testing.py"
 295                        (("/usr/bin/env python") python))))
 296                   %standard-phases)))
 297     (synopsis "Library for numerical linear algebra")
 298     (description
 299      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 300 problems in numerical linear algebra.")
 301     (license (license:non-copyleft "file://LICENSE"
 302                                 "See LICENSE in the distribution."))))
 303
 304 (define-public gnuplot
 305   (package
 306     (name "gnuplot")
 307     (version "4.6.3")
 308     (source
 309      (origin
 310       (method url-fetch)
 311       (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
 312                                 version "/gnuplot-" version ".tar.gz"))
 313       (sha256
 314        (base32
 315         "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
 316     (build-system gnu-build-system)
 317     (inputs `(("readline" ,readline)
 318               ("cairo" ,cairo)
 319               ("pango" ,pango)
 320               ("gd" ,gd)))
 321     (native-inputs `(("texlive" ,texlive)
 322                      ("pkg-config" ,pkg-config)))
 323     (home-page "http://www.gnuplot.info")
 324     (synopsis "Command-line driven graphing utility")
 325     (description "Gnuplot is a portable command-line driven graphing
 326 utility.  It was originally created to allow scientists and students to
 327 visualize mathematical functions and data interactively, but has grown to
 328 support many non-interactive uses such as web scripting.  It is also used as a
 329 plotting engine by third-party applications like Octave.")
 330     ;;  X11 Style with the additional restriction that derived works may only be
 331     ;;  distributed as patches to the original.
 332     (license (license:fsf-free
 333               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
 334
 335 (define-public hdf5
 336   (package
 337     (name "hdf5")
 338     (version "1.8.12")
 339     (source
 340      (origin
 341       (method url-fetch)
 342       (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-"
 343                           version "/src/hdf5-"
 344                           version ".tar.bz2"))
 345       (sha256
 346        (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
 347     (build-system gnu-build-system)
 348     (inputs
 349      `(("zlib" ,zlib)))
 350     (arguments
 351      `(#:phases
 352         (alist-cons-before
 353          'configure 'patch-configure
 354          (lambda _
 355            (substitute* "configure"
 356              (("/bin/mv") "mv")))
 357          %standard-phases)))
 358     (home-page "http://www.hdfgroup.org")
 359     (synopsis "Management suite for extremely large and complex data")
 360     (description "HDF5 is a suite that makes possible the management of
 361 extremely large and complex data collections.")
 362     (license (license:x11-style
 363               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 364
 365
 366 ;; For a fully featured Octave, users  are strongly recommended also to install
 367 ;; the following packages: texinfo, less, ghostscript, gnuplot.
 368 (define-public octave
 369   (package
 370     (name "octave")
 371     (version "3.8.2")
 372     (source
 373      (origin
 374       (method url-fetch)
 375       (uri (string-append "mirror://gnu/octave/octave-"
 376                           version ".tar.gz"))
 377       (sha256
 378        (base32
 379         "05slz8yx8k91fqlnfr1f0vni95iq9qmchz41c7nf4isn3b2fjn7j"))))
 380     (build-system gnu-build-system)
 381     (inputs
 382      `(("lapack" ,lapack)
 383        ("readline" ,readline)
 384        ("glpk" ,glpk)
 385        ("fftw" ,fftw)
 386        ("fftwf" ,fftwf)
 387        ("arpack" ,arpack-ng)
 388        ("curl" ,curl)
 389        ("pcre" ,pcre)
 390        ("fltk" ,fltk)
 391        ("fontconfig" ,fontconfig)
 392        ("freetype" ,freetype)
 393        ("hdf5" ,hdf5)
 394        ("libxft" ,libxft)
 395        ("mesa" ,mesa)
 396        ("glu" ,glu)
 397        ("zlib" ,zlib)))
 398     (native-inputs
 399      `(("gfortran" ,gfortran-4.8)
 400        ("pkg-config" ,pkg-config)
 401        ("perl" ,perl)
 402        ;; The following inputs are not actually used in the build process.
 403        ;; However, the ./configure gratuitously tests for their existence and
 404        ;; assumes that programs not present at build time are also not, and
 405        ;; can never be, available at run time!  If these inputs are therefore
 406        ;; not present, support for them will be built out.  However, Octave
 407        ;; will still run without them, albeit without the features they
 408        ;; provide.
 409        ("less" ,less)
 410        ("texinfo" ,texinfo)
 411        ("ghostscript" ,ghostscript)
 412        ("gnuplot" ,gnuplot)))
 413     (arguments
 414      `(#:configure-flags (list (string-append "--with-shell="
 415                             (assoc-ref %build-inputs "bash")
 416                             "/bin/sh"))))
 417     (home-page "http://www.gnu.org/software/octave/")
 418     (synopsis "High-level language for numerical computation")
 419     (description "GNU Octave is a high-level interpreted language that is
 420 specialized for numerical computations.  It can be used for both linear and
 421 non-linear applications and it provides great support for visualizing results.
 422 Work may be performed both at the interactive command-line as well as via
 423 script files.")
 424     (license license:gpl3+)))
 425
 426 (define-public gmsh
 427   (package
 428     (name "gmsh")
 429     (version "2.8.4")
 430     (source
 431      (origin
 432       (method url-fetch)
 433       (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
 434                           version "-source.tgz"))
 435       (sha256
 436        (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
 437       (modules '((guix build utils)))
 438       (snippet
 439        ;; Remove non-free METIS code
 440        '(delete-file-recursively "contrib/Metis"))))
 441     (build-system cmake-build-system)
 442     (propagated-inputs
 443      `(("fltk" ,fltk)
 444        ("gfortran" ,gfortran-4.8)
 445        ("gmp" ,gmp)
 446        ("hdf5" ,hdf5)
 447        ("lapack" ,lapack)
 448        ("mesa" ,mesa)
 449        ("glu" ,glu)
 450        ("libx11" ,libx11)
 451        ("libxext" ,libxext)))
 452     (arguments
 453      `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
 454                            "-DENABLE_BUILD_SHARED:BOOL=ON"
 455                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
 456     (home-page "http://www.geuz.org/gmsh/")
 457     (synopsis "3D finite element grid generator")
 458     (description "Gmsh is a 3D finite element grid generator with a built-in
 459 CAD engine and post-processor.  Its design goal is to provide a fast, light
 460 and user-friendly meshing tool with parametric input and advanced
 461 visualization capabilities.  Gmsh is built around four modules: geometry,
 462 mesh, solver and post-processing.  The specification of any input to these
 463 modules is done either interactively using the graphical user interface or in
 464 ASCII text files using Gmsh's own scripting language.")
 465     (license license:gpl2+)))
 466
 467 (define-public petsc
 468   (package
 469     (name "petsc")
 470     (version "3.4.4")
 471     (source
 472      (origin
 473       (method url-fetch)
 474       ;; The *-lite-* tarball does not contain the *large* documentation
 475       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
 476                           "petsc-lite-" version ".tar.gz"))
 477       (sha256
 478        (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
 479       (patches
 480        (list (search-patch "petsc-fix-threadcomm.patch")))))
 481     (build-system gnu-build-system)
 482     (native-inputs
 483      `(("python" ,python-2)
 484        ("perl" ,perl)))
 485     (inputs
 486      `(("gfortran" ,gfortran-4.8)
 487        ("lapack" ,lapack)
 488        ("superlu" ,superlu)
 489        ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
 490        ;; leaving out opengl, as configuration seems to only be for mac
 491        ))
 492     (arguments
 493      `(#:test-target "test"
 494        #:parallel-build? #f
 495        #:configure-flags
 496        `("--with-mpi=0"
 497          "--with-openmp=1"
 498          "--with-superlu=1"
 499          ,(string-append "--with-superlu-include="
 500                          (assoc-ref %build-inputs "superlu") "/include")
 501          ,(string-append "--with-superlu-lib="
 502                          (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
 503        #:phases
 504        (alist-replace
 505         'configure
 506         ;; PETSc's configure script is actually a python script, so we can't
 507         ;; run it with bash.
 508         (lambda* (#:key outputs (configure-flags '())
 509                   #:allow-other-keys)
 510           (let* ((prefix (assoc-ref outputs "out"))
 511                  (flags `(,(string-append "--prefix=" prefix)
 512                           ,@configure-flags)))
 513             (format #t "build directory: ~s~%" (getcwd))
 514             (format #t "configure flags: ~s~%" flags)
 515             (zero? (apply system* "./configure" flags))))
 516         (alist-cons-after
 517          'configure 'clean-local-references
 518          ;; Try to keep build directory names from leaking into compiled code
 519          (lambda* (#:key inputs outputs #:allow-other-keys)
 520            (let ((out (assoc-ref outputs "out")))
 521              (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
 522                (((getcwd)) out))))
 523          (alist-cons-after
 524           'install 'clean-install
 525           ;; Try to keep installed files from leaking build directory names.
 526           (lambda* (#:key inputs outputs #:allow-other-keys)
 527             (let ((out     (assoc-ref outputs "out"))
 528                   (fortran (assoc-ref inputs  "gfortran")))
 529               (substitute* (map (lambda (file)
 530                                   (string-append out "/" file))
 531                                 '("conf/petscvariables"
 532                                   "conf/PETScConfig.cmake"))
 533                 (((getcwd)) out))
 534               ;; Make compiler references point to the store
 535               (substitute* (string-append out "/conf/petscvariables")
 536                 (("= g(cc|\\+\\+|fortran)" _ suffix)
 537                  (string-append "= " fortran "/bin/g" suffix)))
 538               ;; PETSc installs some build logs, which aren't necessary.
 539               (for-each (lambda (file)
 540                           (let ((f (string-append out "/" file)))
 541                             (when (file-exists? f)
 542                               (delete-file f))))
 543                         '("conf/configure.log"
 544                           "conf/make.log"
 545                           "conf/test.log"
 546                           "conf/error.log"
 547                           "conf/RDict.db"
 548                           ;; Once installed, should uninstall with Guix
 549                           "conf/uninstall.py"))))
 550           %standard-phases)))))
 551     (home-page "http://www.mcs.anl.gov/petsc")
 552     (synopsis "Library to solve PDEs")
 553     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
 554 data structures and routines for the scalable (parallel) solution of
 555 scientific applications modeled by partial differential equations.")
 556     (license (license:non-copyleft
 557               "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
 558
 559 (define-public petsc-complex
 560   (package (inherit petsc)
 561     (location (source-properties->location (current-source-location)))
 562     (name "petsc-complex")
 563     (arguments
 564      (substitute-keyword-arguments (package-arguments petsc)
 565        ((#:configure-flags cf)
 566         `(cons "--with-scalar-type=complex" ,cf))))
 567     (synopsis "Library to solve PDEs (with complex scalars)")))
 568
 569 (define-public petsc-openmpi
 570   (package (inherit petsc)
 571     (name "petsc-openmpi")
 572     (inputs
 573      `(("openmpi" ,openmpi)
 574        ,@(package-inputs petsc)))
 575     (arguments
 576      (substitute-keyword-arguments (package-arguments petsc)
 577        ((#:configure-flags cf)
 578         ``("--with-mpiexec=mpirun"
 579            ,(string-append "--with-mpi-dir="
 580                            (assoc-ref %build-inputs "openmpi"))
 581            ,@(delete "--with-mpi=0" ,cf)))))
 582     (synopsis "Library to solve PDEs (with MPI support)")))
 583
 584 (define-public petsc-complex-openmpi
 585   (package (inherit petsc-complex)
 586     (name "petsc-complex-openmpi")
 587     (inputs
 588      `(("openmpi" ,openmpi)
 589        ,@(package-inputs petsc-complex)))
 590     (arguments
 591      (substitute-keyword-arguments (package-arguments petsc-complex)
 592        ((#:configure-flags cf)
 593         ``("--with-mpiexec=mpirun"
 594            ,(string-append "--with-mpi-dir="
 595                            (assoc-ref %build-inputs "openmpi"))
 596            ,@(delete "--with-mpi=0" ,cf)))))
 597     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 598
 599 (define-public superlu
 600   (package
 601     (name "superlu")
 602     (version "4.3")
 603     (source
 604      (origin
 605        (method url-fetch)
 606        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
 607                            "superlu_" version ".tar.gz"))
 608        (sha256
 609         (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n"))))
 610     (build-system gnu-build-system)
 611     (native-inputs
 612      `(("tcsh" ,tcsh)))
 613     (inputs
 614      `(("lapack" ,lapack)
 615        ("gfortran" ,gfortran-4.8)))
 616     (arguments
 617      `(#:parallel-build? #f
 618        #:tests? #f                      ;tests are run as part of `make all`
 619        #:phases
 620        (alist-replace
 621         'configure
 622         (lambda* (#:key inputs outputs #:allow-other-keys)
 623           (call-with-output-file "make.inc"
 624             (lambda (port)
 625               (format port "
 626 PLAT        =
 627 SuperLUroot = ~a
 628 SUPERLULIB  = ~a/lib/libsuperlu.a
 629 TMGLIB      = libtmglib.a
 630 BLASDEF     = -DUSE_VENDOR_BLAS
 631 BLASLIB     = -L~a/lib -lblas
 632 LIBS        = $(SUPERLULIB) $(BLASLIB)
 633 ARCH        = ar
 634 ARCHFLAGS   = cr
 635 RANLIB      = ranlib
 636 CC          = gcc
 637 PIC         = -fPIC
 638 CFLAGS      = -O3 -DPRNTlevel=0 $(PIC)
 639 NOOPTS      = -O0 $(PIC)
 640 FORTRAN     = gfortran
 641 FFLAGS      = -O2 $(PIC)
 642 LOADER      = $(CC)
 643 CDEFS       = -DAdd_"
 644                       (getcwd)
 645                       (assoc-ref outputs "out")
 646                       (assoc-ref inputs "lapack")))))
 647         (alist-cons-before
 648          'build 'create-install-directories
 649          (lambda* (#:key outputs #:allow-other-keys)
 650            (for-each
 651             (lambda (dir)
 652               (mkdir-p (string-append (assoc-ref outputs "out")
 653                                       "/" dir)))
 654             '("lib" "include")))
 655          (alist-replace
 656           'install
 657           (lambda* (#:key outputs #:allow-other-keys)
 658             ;; Library is placed in lib during the build phase.  Copy over
 659             ;; headers to include.
 660             (let* ((out    (assoc-ref outputs "out"))
 661                    (incdir (string-append out "/include")))
 662               (for-each (lambda (file)
 663                           (let ((base (basename file)))
 664                             (format #t "installing `~a' to `~a'~%"
 665                                     base incdir)
 666                             (copy-file file
 667                                        (string-append incdir "/" base))))
 668                         (find-files "SRC" ".*\\.h$"))))
 669           %standard-phases)))))
 670     (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
 671     (synopsis "Supernodal direct solver for sparse linear systems")
 672     (description
 673      "SuperLU is a general purpose library for the direct solution of large,
 674 sparse, nonsymmetric systems of linear equations on high performance machines.
 675 The library is written in C and is callable from either C or Fortran.  The
 676 library routines perform an LU decomposition with partial pivoting and
 677 triangular system solves through forward and back substitution.  The library
 678 also provides threshold-based ILU factorization preconditioners.")
 679     (license license:bsd-3)))
 680
 681 (define-public superlu-dist
 682   (package
 683     (name "superlu-dist")
 684     (version "3.3")
 685     (source
 686      (origin
 687        (method url-fetch)
 688        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
 689                            "superlu_dist_" version ".tar.gz"))
 690        (sha256
 691         (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
 692        (patches (list (search-patch "superlu-dist-scotchmetis.patch")))))
 693     (build-system gnu-build-system)
 694     (native-inputs
 695      `(("tcsh" ,tcsh)))
 696     (inputs
 697      `(("gfortran" ,gfortran-4.8)))
 698     (propagated-inputs
 699      `(("openmpi" ,openmpi)             ;headers include MPI heades
 700        ("lapack" ,lapack)               ;required to link with output library
 701        ("pt-scotch" ,pt-scotch)))       ;same
 702     (arguments
 703      `(#:parallel-build? #f             ;race conditions using ar
 704        #:phases
 705        (alist-replace
 706         'configure
 707         (lambda* (#:key inputs outputs #:allow-other-keys)
 708           (call-with-output-file "make.inc"
 709             (lambda (port)
 710               (format port "
 711 PLAT        =
 712 DSuperLUroot = ~a
 713 DSUPERLULIB  = ~a/lib/libsuperlu_dist.a
 714 BLASDEF     = -DUSE_VENDOR_BLAS
 715 BLASLIB     = -L~a/lib -lblas
 716 PARMETISLIB = -L~a/lib \
 717               -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
 718               -lscotch -lscotcherr -lscotcherrexit
 719 METISLIB    = -L~:*~a/lib \
 720               -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
 721 LIBS        = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
 722 ARCH        = ar
 723 ARCHFLAGS   = cr
 724 RANLIB      = ranlib
 725 CC          = mpicc
 726 PIC         = -fPIC
 727 CFLAGS      = -O3 -g -DPRNTlevel=0 $(PIC)
 728 NOOPTS      = -O0 -g $(PIC)
 729 FORTRAN     = mpifort
 730 FFLAGS      = -O2 -g $(PIC)
 731 LOADER      = $(CC)
 732 CDEFS       = -DAdd_"
 733                       (getcwd)
 734                       (assoc-ref outputs "out")
 735                       (assoc-ref inputs "lapack")
 736                       (assoc-ref inputs "pt-scotch")))))
 737         (alist-cons-after
 738          'unpack 'remove-broken-symlinks
 739          (lambda _
 740            (for-each delete-file
 741                      (find-files "MAKE_INC" "\\.#make\\..*")))
 742          (alist-cons-before
 743           'build 'create-install-directories
 744           (lambda* (#:key outputs #:allow-other-keys)
 745             (for-each
 746              (lambda (dir)
 747                (mkdir-p (string-append (assoc-ref outputs "out")
 748                                        "/" dir)))
 749              '("lib" "include")))
 750           (alist-replace
 751            'check
 752            (lambda _
 753              (with-directory-excursion "EXAMPLE"
 754                (and
 755                 (zero? (system* "mpirun" "-n" "2"
 756                                 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
 757                 (zero? (system* "mpirun" "-n" "2"
 758                                 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
 759            (alist-replace
 760             'install
 761             (lambda* (#:key outputs #:allow-other-keys)
 762               ;; Library is placed in lib during the build phase.  Copy over
 763               ;; headers to include.
 764               (let* ((out    (assoc-ref outputs "out"))
 765                      (incdir (string-append out "/include")))
 766                 (for-each (lambda (file)
 767                             (let ((base (basename file)))
 768                               (format #t "installing `~a' to `~a'~%"
 769                                       base incdir)
 770                               (copy-file file
 771                                          (string-append incdir "/" base))))
 772                           (find-files "SRC" ".*\\.h$"))))
 773             %standard-phases)))))))
 774     (home-page (package-home-page superlu))
 775     (synopsis "Parallel supernodal direct solver")
 776     (description
 777      "SuperLU_DIST is a parallel extension to the serial SuperLU library.
 778 It is targeted for distributed memory parallel machines.  SuperLU_DIST is
 779 implemented in ANSI C, and MPI for communications.")
 780     (license license:bsd-3)))
 781
 782 (define-public scotch
 783   (package
 784     (name "scotch")
 785     (version "6.0.0")
 786     (source
 787      (origin
 788       (method url-fetch)
 789       (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/"
 790                           "scotch_" version ".tar.gz"))
 791       (sha256
 792        (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
 793       (patches (list (search-patch "scotch-test-threading.patch")))))
 794     (build-system gnu-build-system)
 795     (inputs
 796      `(("zlib" ,zlib)
 797        ("flex" ,flex)
 798        ("bison" ,bison)))
 799     (arguments
 800      `(#:phases
 801        (alist-cons-after
 802         'unpack 'chdir-to-src
 803         (lambda _ (chdir "src"))
 804         (alist-replace
 805          'configure
 806          (lambda _
 807            (call-with-output-file "Makefile.inc"
 808              (lambda (port)
 809                (format port "
 810 EXE =
 811 LIB = .a
 812 OBJ = .o
 813 MAKE = make
 814 AR = ar
 815 ARFLAGS = -ruv
 816 CCS = gcc
 817 CCP = mpicc
 818 CCD = gcc
 819 CPPFLAGS =~{ -D~a~}
 820 CFLAGS = -O2 -g $(CPPFLAGS)
 821 LDFLAGS = -lz -lm -lrt -lpthread
 822 CP = cp
 823 LEX = flex -Pscotchyy -olex.yy.c
 824 LN = ln
 825 MKDIR = mkdir
 826 MV = mv
 827 RANLIB = ranlib
 828 YACC = bison -pscotchyy -y -b y
 829 "
 830                        '("COMMON_FILE_COMPRESS_GZ"
 831                          "COMMON_PTHREAD"
 832                          "COMMON_RANDOM_FIXED_SEED"
 833                          ;; TODO: Define once our MPI supports
 834                          ;; MPI_THREAD_MULTIPLE
 835                          ;; "SCOTCH_PTHREAD"
 836                          ;; "SCOTCH_PTHREAD_NUMBER=2"
 837                          "restrict=__restrict")))))
 838          (alist-replace
 839           'install
 840           (lambda* (#:key outputs #:allow-other-keys)
 841             (let ((out (assoc-ref outputs "out")))
 842               (mkdir out)
 843               (zero? (system* "make"
 844                               (string-append "prefix=" out)
 845                               "install"))))
 846           %standard-phases)))))
 847     (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
 848     (synopsis "Programs and libraries for graph algorithms")
 849     (description "SCOTCH is a set of programs and libraries which implement
 850 the static mapping and sparse matrix reordering algorithms developed within
 851 the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
 852 conquer approach, to scientific computing problems such as graph and mesh
 853 partitioning, static mapping, and sparse matrix ordering, in application
 854 domains ranging from structural mechanics to operating systems or
 855 bio-chemistry.")
 856     ;; See LICENSE_en.txt
 857     (license license:cecill-c)))
 858
 859 (define-public pt-scotch
 860   (package (inherit scotch)
 861     (name "pt-scotch")
 862     (propagated-inputs
 863      `(("openmpi" ,openmpi)))           ;Headers include MPI headers
 864     (arguments
 865      (substitute-keyword-arguments (package-arguments scotch)
 866        ((#:phases scotch-phases)
 867         `(alist-replace
 868           'build
 869           ;; TODO: Would like to add parallelism here
 870           (lambda _
 871             (and
 872              (zero? (system* "make" "ptscotch"))
 873              ;; Install the serial metis compatibility library
 874              (zero? (system* "make" "-C" "libscotchmetis" "install"))))
 875           (alist-replace
 876            'check
 877            (lambda _ (zero? (system* "make" "ptcheck")))
 878            (alist-replace
 879             'install
 880             (lambda* (#:key outputs #:allow-other-keys)
 881               (let ((out (assoc-ref outputs "out")))
 882                 (mkdir out)
 883                 (zero? (system* "make"
 884                                 (string-append "prefix=" out)
 885                                 "install"))))
 886             ,scotch-phases))))))
 887     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
 888
 889 (define-public gsegrafix
 890   (package
 891     (name "gsegrafix")
 892     (version "1.0.6")
 893     (source
 894      (origin
 895       (method url-fetch)
 896       (uri (string-append "mirror://gnu/" name "/" name "-"
 897                           version ".tar.gz"))
 898       (sha256
 899        (base32
 900         "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
 901     (build-system gnu-build-system)
 902     (arguments
 903      `(#:configure-flags '("LDFLAGS=-lm")))
 904     (inputs
 905      `(("libgnomecanvas" ,libgnomecanvas)
 906        ("libbonoboui" ,libbonoboui)
 907        ("libgnomeui" ,libgnomeui)
 908        ("libgnomeprintui" ,libgnomeprintui)
 909        ("popt" ,popt)))
 910     (native-inputs
 911      `(("pkg-config" ,pkg-config)))
 912     (home-page "http://www.gnu.org/software/gsegrafix/")
 913     (synopsis "GNOME application to create scientific and engineering plots")
 914     (description  "GSEGrafix is an application which produces high-quality graphical
 915 plots for science and engineering.  Plots are specified via simple ASCII
 916 parameter files and data files and are presented in an anti-aliased GNOME
 917 canvas.  The program supports rectangular two-dimensional plots, histograms,
 918 polar-axis plots and three-dimensional plots.  Plots can be printed or saved
 919 to BMP, JPEG or PNG image formats.")
 920     (license license:gpl3+)))
 921
 922 (define-public maxima
 923   (package
 924     (name "maxima")
 925     (version "5.34.1")
 926     (source
 927      (origin
 928        (method url-fetch)
 929        (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
 930                            version "-source/" name "-" version ".tar.gz"))
 931        (sha256
 932         (base32
 933          "1dw9vfzldpj7lv303xbw0wpyn6ra6i2yzwlrjbcx7j0jm5n43ji0"))))
 934     (build-system gnu-build-system)
 935     (inputs
 936      `(("gcl" ,gcl)
 937        ("gnuplot" ,gnuplot)                       ;for plots
 938        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
 939     (native-inputs
 940      `(("texinfo" ,texinfo)
 941        ("perl" ,perl)))
 942     (arguments
 943      `(#:configure-flags
 944        (list "--enable-gcl"
 945              (string-append "--with-posix-shell="
 946                             (assoc-ref %build-inputs "bash")
 947                             "/bin/sh")
 948              (string-append "--with-wish="
 949                             (assoc-ref %build-inputs "tk")
 950                             "/bin/wish"
 951                             (let ((v ,(package-version tk)))
 952                               (string-take v (string-index-right v #\.)))))
 953        ;; By default Maxima attempts to write temporary files to
 954        ;; '/tmp/nix-build-maxima-5.34.1', which doesn't exist.  Work around
 955        ;; that.
 956        #:make-flags (list "TMPDIR=/tmp")
 957        #:phases (alist-cons-before
 958                  'check 'pre-check
 959                  (lambda _
 960                    (chmod "src/maxima" #o555))
 961                  ;; Make sure the doc and emacs files are found in the
 962                  ;; standard location.  Also configure maxima to find gnuplot
 963                  ;; without having it on the PATH.
 964                  (alist-cons-after
 965                   'install 'post-install
 966                   (lambda* (#:key outputs inputs #:allow-other-keys)
 967                     (let* ((gnuplot (assoc-ref inputs "gnuplot"))
 968                           (out (assoc-ref outputs "out"))
 969                           (datadir (string-append out "/share/maxima/" ,version)))
 970                       (with-directory-excursion out
 971                         (mkdir-p "share/emacs")
 972                         (mkdir-p "share/doc")
 973                         (symlink
 974                          (string-append datadir "/emacs/")
 975                          (string-append out "/share/emacs/site-lisp"))
 976                         (symlink
 977                          (string-append datadir "/doc/")
 978                          (string-append out "/share/doc/maxima"))
 979                         (with-atomic-file-replacement
 980                          (string-append datadir "/share/maxima-init.lisp")
 981                          (lambda (in out)
 982                            (format out "~a ~s~a~%"
 983                                    "(setf $gnuplot_command "
 984                                    (string-append gnuplot "/bin/gnuplot") ")")
 985                            (dump-port in out))))))
 986                   %standard-phases))))
 987     (home-page "http://maxima.sourceforge.net")
 988     (synopsis "Numeric and symbolic expression manipulation")
 989     (description "Maxima is a system for the manipulation of symbolic and
 990 numerical expressions.  It yields high precision numeric results by using
 991 exact fractions, arbitrary precision integers, and variable precision floating
 992 point numbers")
 993     ;; Some files are lgpl2.1+. Some are gpl2+.  Some explicitly state gpl1+.
 994     ;; Others simply say "GNU General Public License" without stating a
 995     ;; version (which implicitly means gpl1+).
 996     ;; At least one file (src/maxima.asd) says "version 2."
 997     ;; GPLv2 only is therefore the smallest subset.
 998     (license license:gpl2)))
 999
1000 (define-public muparser
1001   (package
1002     (name "muparser")
1003     (version "2.2.5")
1004     (source
1005      (origin
1006        (method svn-fetch)
1007        (uri (svn-reference
1008              (url "http://muparser.googlecode.com/svn/trunk/")
1009              (revision 34)))
1010        (sha256
1011         (base32
1012          "1d6bdbhx9zj3srwj3m7c9hvr18gnx1fx43h6d25my7q85gicpcwn"))))
1013     (build-system gnu-build-system)
1014     (arguments
1015      `(#:configure-flags '("--enable-samples=no")
1016        #:tests? #f)) ;no "check" target
1017     (home-page "http://muparser.beltoforion.de/")
1018     (synopsis "Fast parser library for mathematical expressions")
1019     (description
1020      "muParser is an extensible high performance math parser library.  It is
1021 based on transforming an expression into a bytecode and precalculating
1022 constant parts of it.")
1023     (license license:expat)))
1024
1025 (define-public openblas
1026   (package
1027     (name "openblas")
1028     (version "0.2.14")
1029     (source
1030      (origin
1031        (method url-fetch)
1032        (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
1033                            version))
1034        (file-name (string-append name "-" version ".tar.gz"))
1035        (sha256
1036         (base32
1037          "0av3pd96j8rx5i65f652xv9wqfkaqn0w4ma1gvbyz73i6j2hi9db"))))
1038     (build-system gnu-build-system)
1039     (arguments
1040      `(#:tests? #f  ;no "check" target
1041        ;; DYNAMIC_ARCH is not supported on MIPS.  When it is disabled,
1042        ;; OpenBLAS will tune itself to the build host, so we need to disable
1043        ;; substitutions.
1044        #:substitutable? ,(not (string-prefix? "mips" (%current-system)))
1045        #:make-flags
1046        (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
1047              "SHELL=bash"
1048              "NO_LAPACK=1"
1049              ;; Build the library for all supported CPUs.  This allows
1050              ;; switching CPU targets at runtime with the environment variable
1051              ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
1052              ;; Unfortunately, this is not supported on MIPS.
1053              ,@(if (string-prefix? "mips" (%current-system))
1054                    '()
1055                    '("DYNAMIC_ARCH=1")))
1056        ;; no configure script
1057        #:phases (alist-delete 'configure %standard-phases)))
1058     (inputs
1059      `(("fortran" ,gfortran-4.8)))
1060     (native-inputs
1061      `(("cunit" ,cunit)
1062        ("perl" ,perl)))
1063     (home-page "http://www.openblas.net/")
1064     (synopsis "Optimized BLAS library based on GotoBLAS")
1065     (description
1066      "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
1067     (license license:bsd-3)))
1068
1069 (define-public openlibm
1070   (package
1071     (name "openlibm")
1072     (version "0.4.1")
1073     (source
1074      (origin
1075        (method url-fetch)
1076        (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
1077                            version ".tar.gz"))
1078        (file-name (string-append name "-" version ".tar.gz"))
1079        (sha256
1080         (base32
1081          "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn"))))
1082     (build-system gnu-build-system)
1083     (arguments
1084      `(#:make-flags
1085        (list (string-append "prefix=" (assoc-ref %outputs "out")))
1086        #:phases
1087        ;; no configure script
1088        (alist-delete 'configure %standard-phases)
1089        #:tests? #f)) ;the tests are part of the default target
1090     (home-page "http://openlibm.org/")
1091     (synopsis "Portable C mathematical library (libm)")
1092     (description
1093      "OpenLibm is an effort to have a high quality, portable, standalone C
1094 mathematical library (libm).  It can be used standalone in applications and
1095 programming language implementations.  The project was born out of a need to
1096 have a good libm for the Julia programming langage that worked consistently
1097 across compilers and operating systems, and in 32-bit and 64-bit
1098 environments.")
1099     ;; See LICENSE.md for details.
1100     (license (list license:expat
1101                    license:isc
1102                    license:bsd-2
1103                    license:public-domain
1104                    license:lgpl2.1+))))
1105
1106 (define-public openspecfun
1107   (package
1108     (name "openspecfun")
1109     (version "0.4")
1110     (source
1111      (origin
1112        (method url-fetch)
1113        (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
1114                            version ".tar.gz"))
1115        (file-name (string-append name "-" version ".tar.gz"))
1116        (sha256
1117         (base32
1118          "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z"))))
1119     (build-system gnu-build-system)
1120     (arguments
1121      '(#:tests? #f  ;no "check" target
1122        #:make-flags
1123        (list (string-append "prefix=" (assoc-ref %outputs "out")))
1124        ;; no configure script
1125        #:phases (alist-delete 'configure %standard-phases)))
1126     (inputs
1127      `(("fortran" ,gfortran-4.8)))
1128     (home-page "https://github.com/JuliaLang/openspecfun")
1129     (synopsis "Collection of special mathematical functions")
1130     (description
1131      "Openspecfun provides AMOS and Faddeeva.  AMOS (from Netlib) is a
1132 portable package for Bessel Functions of a Complex Argument and Nonnegative
1133 Order; it contains subroutines for computing Bessel functions and Airy
1134 functions.  Faddeeva allows computing the various error functions of arbitrary
1135 complex arguments (Faddeeva function, error function, complementary error
1136 function, scaled complementary error function, imaginary error function, and
1137 Dawson function); given these, one can also easily compute Voigt functions,
1138 Fresnel integrals, and similar related functions as well.")
1139     ;; Faddeeva is released under the Expat license; AMOS is included as
1140     ;; public domain software.
1141     (license (list license:expat license:public-domain))))
1142
1143 (define-public suitesparse
1144   (package
1145     (name "suitesparse")
1146     (version "4.4.3")
1147     (source
1148      (origin
1149        (method url-fetch)
1150        (uri (string-append
1151              "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
1152              version ".tar.gz"))
1153        (sha256
1154         (base32
1155          "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
1156     (build-system gnu-build-system)
1157     (arguments
1158      '(#:parallel-build? #f ;cholmod build fails otherwise
1159        #:tests? #f  ;no "check" target
1160        #:make-flags
1161        (list "CC=gcc"
1162              "BLAS=-lblas"
1163              "TBB=-ltbb"
1164              "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
1165              (string-append "INSTALL_LIB="
1166                             (assoc-ref %outputs "out") "/lib")
1167              (string-append "INSTALL_INCLUDE="
1168                             (assoc-ref %outputs "out") "/include"))
1169        #:phases
1170        (alist-cons-before
1171         'install 'prepare-out
1172         ;; README.txt states that the target directories must exist prior to
1173         ;; running "make install".
1174         (lambda _
1175           (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
1176           (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
1177         ;; no configure script
1178         (alist-delete 'configure %standard-phases))))
1179     (inputs
1180      `(("tbb" ,tbb)
1181        ("lapack" ,lapack)))
1182     (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
1183     (synopsis "Suite of sparse matrix software")
1184     (description
1185      "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
1186 multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
1187 multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
1188 simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
1189 CXSparse, a concise sparse Cholesky factorization package; and many other
1190 packages.")
1191     ;; LGPLv2.1+:
1192     ;;   AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
1193     ;; GPLv2+:
1194     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
1195     (license (list license:gpl2+ license:lgpl2.1+))))
1196
1197 (define-public atlas
1198   (package
1199     (name "atlas")
1200     (version "3.10.2")
1201     (source (origin
1202               (method url-fetch)
1203               (uri (string-append "mirror://sourceforge/math-atlas/atlas"
1204                                   version ".tar.bz2"))
1205               (sha256
1206                (base32
1207                 "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars"))))
1208     (build-system gnu-build-system)
1209     (home-page "http://math-atlas.sourceforge.net/")
1210     (inputs `(("gfortran" ,gfortran-4.8)
1211               ("lapack-tar" ,(package-source lapack))))
1212     (outputs '("out" "doc"))
1213     ;; For the moment we drop support for MIPS at it fails to compile. See
1214     ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
1215     (supported-systems (delete "mips64el-linux" %supported-systems))
1216     (arguments
1217      `(#:parallel-build? #f
1218        #:parallel-tests? #f
1219
1220        ;; ATLAS tunes itself for the machine it is built on, as explained at
1221        ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
1222        ;; For this reason, we want users to build it locally instead of using
1223        ;; substitutes.
1224        #:substitutable? #f
1225
1226        #:modules ((srfi srfi-26)
1227                   (srfi srfi-1)
1228                   (guix build gnu-build-system)
1229                   (guix build utils))
1230        #:configure-flags
1231        `(;; Generate position independent code suitable for dynamic libraries
1232          ;; and use WALL timer to get more accurate timing.
1233          "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
1234          ;; Set word width.
1235          "-b"
1236          ,,(if (string-match "64" (%current-system))
1237                "64"
1238                "32")
1239          ;; Disable parallel build as it gives errors: atlas_pthread.h is
1240          ;; needed to compile C files before it is generated.
1241          "-Ss" "pmake" "make -j 1"
1242          ;; Probe is failing for MIPS.  We therefore define the system
1243          ;; architecture explicitly by setting (-A) MACHINETYPE = 49
1244          ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
1245          ,,@(if (string-prefix? "mips" (%current-system))
1246               (list "-A" "49" "-V" "1")
1247               (list))
1248          ;; Generate shared libraries.
1249          "--shared"
1250          ;; Build a full LAPACK library.
1251          ,(string-append "--with-netlib-lapack-tarfile="
1252                          (assoc-ref %build-inputs "lapack-tar")))
1253        #:phases
1254         (alist-cons-after
1255          'install 'install-doc
1256          (lambda* (#:key outputs inputs #:allow-other-keys)
1257            (let ((doc (string-append (assoc-ref outputs "doc")
1258                                      "/share/doc/atlas")))
1259              (mkdir-p doc)
1260              (fold (lambda (file previous)
1261                      (and previous (zero? (system* "cp" file doc))))
1262                    #t (find-files "../ATLAS/doc" ".*"))))
1263          (alist-cons-after
1264           'check 'check-pt
1265           (lambda _ (zero? (system* "make" "ptcheck")))
1266           ;; Fix files required to run configure.
1267           (alist-cons-before
1268            'configure 'fix-/bin/sh
1269            (lambda _
1270              ;; Use `sh', not `/bin/sh'.
1271              (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
1272                (("/bin/sh")
1273                 "sh")))
1274            ;; Fix /bin/sh in generated make files.
1275            (alist-cons-after
1276             'configure 'fix-/bin/sh-in-generated-files
1277             (lambda _
1278               (substitute* (find-files "." "^[Mm]ake\\.inc.*")
1279                 (("/bin/sh")
1280                  "sh")))
1281             ;; ATLAS configure program does not accepts the default flags
1282             ;; passed by the 'gnu-build-system'.
1283             (alist-replace
1284              'configure
1285              (lambda* (#:key native-inputs inputs outputs
1286                              (configure-flags '())
1287                              #:allow-other-keys #:rest args)
1288                (let* ((prefix     (assoc-ref outputs "out"))
1289                       (bash       (or (and=> (assoc-ref
1290                                               (or native-inputs inputs) "bash")
1291                                              (cut string-append <> "/bin/bash"))
1292                                       "/bin/sh"))
1293                       (flags      `(,(string-append "--prefix=" prefix)
1294                                     ,@configure-flags))
1295                       (abs-srcdir (getcwd))
1296                       (srcdir     (string-append "../" (basename abs-srcdir))))
1297                  (format #t "source directory: ~s (relative from build: ~s)~%"
1298                          abs-srcdir srcdir)
1299                  (mkdir "../build")
1300                  (chdir "../build")
1301                  (format #t "build directory: ~s~%" (getcwd))
1302                  (format #t "configure flags: ~s~%" flags)
1303                  (zero? (apply system* bash
1304                                (string-append srcdir "/configure")
1305                                flags))))
1306              %standard-phases)))))))
1307     (synopsis "Automatically Tuned Linear Algebra Software")
1308     (description
1309      "ATLAS is an automatically tuned linear algebra software library
1310 providing C and Fortran77 interfaces to a portably efficient BLAS
1311 implementation, as well as a few routines from LAPACK.
1312
1313 Optimization occurs at build time.  For this reason, the library is built on
1314 the machine where it is installed, without resorting to pre-built substitutes.
1315
1316 Before building the library, CPU throttling should be disabled.  This can be
1317 done in the BIOS, or, on GNU/Linux, with the following commands:
1318
1319 cpufreq-selector -g performance -c 0
1320 ...
1321 cpufreq-selector -g performance -c N-1
1322
1323 where N is the number of cores of your CPU.  Failure to do so will result in a
1324 library with poor performance.")
1325     (license license:bsd-3)))
1326
1327 (define-public glm
1328   (package
1329     (name "glm")
1330     (version "0.9.6.3")
1331     (source
1332      (origin
1333        (method url-fetch)
1334       (uri (string-append "mirror://sourceforge/ogl-math/glm-"
1335                           version ".zip"))
1336        (sha256
1337         (base32
1338          "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
1339     (build-system cmake-build-system)
1340     (native-inputs
1341      `(("unzip" ,unzip)))
1342     (home-page "http://glm.g-truc.net")
1343     (synopsis "OpenGL Mathematics library")
1344     (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
1345 library for graphics software based on the OpenGL Shading Language (GLSL)
1346 specifications.")
1347     (license license:expat)))
1348
1349 (define-public lpsolve
1350   (package
1351     (name "lpsolve")
1352     (version "5.5.2.0")
1353     (source
1354      (origin
1355       (method url-fetch)
1356       (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
1357                           "/lp_solve_" version "_source.tar.gz"))
1358       (sha256
1359        (base32
1360         "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
1361       (modules '((guix build utils)))
1362       (snippet
1363        '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
1364           (("^c=cc") "c=gcc")
1365           ;; Pretend to be on a 64 bit platform to obtain a common directory
1366           ;; name for the build results on all architectures; nothing else
1367           ;; seems to depend on it.
1368           (("^PLATFORM=.*$") "PLATFORM=ux64\n")))))
1369     (build-system gnu-build-system)
1370     (arguments
1371      `(#:tests? #f ; no check target
1372        #:phases
1373        (modify-phases %standard-phases
1374          (delete 'configure)
1375          (replace 'build
1376            (lambda _
1377              (with-directory-excursion "lpsolve55"
1378                (system* "bash" "ccc"))
1379              (with-directory-excursion "lp_solve"
1380                (system* "bash" "ccc"))
1381              #t))
1382          (replace 'install
1383            (lambda* (#:key outputs #:allow-other-keys)
1384              (let* ((out (assoc-ref outputs "out"))
1385                     (bin (string-append out "/bin"))
1386                     (lib (string-append out "/lib"))
1387                     ;; This is where LibreOffice expects to find the header
1388                     ;; files, and where they are installed by Debian.
1389                     (include (string-append out "/include/lpsolve")))
1390                (mkdir-p lib)
1391                (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
1392                           (string-append lib "/liblpsolve55.a"))
1393                (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
1394                           (string-append lib "/liblpsolve55.so"))
1395                (mkdir-p bin)
1396                (copy-file "lp_solve/bin/ux64/lp_solve"
1397                           (string-append bin "/lp_solve"))
1398                (mkdir-p include)
1399                ;; Install a subset of the header files as on Debian
1400                ;; (plus lp_bit.h, which matches the regular expression).
1401                (for-each
1402                  (lambda (name)
1403                    (copy-file name (string-append include "/" name)))
1404                  (find-files "." "lp_[HMSa-z].*\\.h$"))
1405                (with-directory-excursion "shared"
1406                  (for-each
1407                    (lambda (name)
1408                      (copy-file name (string-append include "/" name)))
1409                    (find-files "." "\\.h$")))
1410                #t))))))
1411     (home-page "http://lpsolve.sourceforge.net/")
1412     (synopsis "Mixed integer linear programming (MILP) solver")
1413     (description
1414      "lp_solve is a mixed integer linear programming solver based on the
1415 revised simplex and the branch-and-bound methods.")
1416     (license license:lgpl2.1+)))