gnu/packages/maths.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2013, 2014 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 ;;;
  10 ;;; This file is part of GNU Guix.
  11 ;;;
  12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  13 ;;; under the terms of the GNU General Public License as published by
  14 ;;; the Free Software Foundation; either version 3 of the License, or (at
  15 ;;; your option) any later version.
  16 ;;;
  17 ;;; GNU Guix is distributed in the hope that it will be useful, but
  18 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;;; GNU General Public License for more details.
  21 ;;;
  22 ;;; You should have received a copy of the GNU General Public License
  23 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  24
  25 (define-module (gnu packages maths)
  26   #:use-module (ice-9 regex)
  27   #:use-module (gnu packages)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (guix packages)
  30   #:use-module (guix download)
  31   #:use-module (guix utils)
  32   #:use-module (guix build-system cmake)
  33   #:use-module (guix build-system gnu)
  34   #:use-module (gnu packages algebra)
  35   #:use-module (gnu packages bison)
  36   #:use-module (gnu packages cmake)
  37   #:use-module (gnu packages compression)
  38   #:use-module (gnu packages curl)
  39   #:use-module (gnu packages elf)
  40   #:use-module (gnu packages flex)
  41   #:use-module (gnu packages fltk)
  42   #:use-module (gnu packages fontutils)
  43   #:use-module (gnu packages gettext)
  44   #:use-module (gnu packages gcc)
  45   #:use-module (gnu packages gd)
  46   #:use-module (gnu packages ghostscript)
  47   #:use-module (gnu packages glib)
  48   #:use-module (gnu packages gtk)
  49   #:use-module (gnu packages less)
  50   #:use-module (gnu packages lisp)
  51   #:use-module (gnu packages gnome)
  52   #:use-module (gnu packages xorg)
  53   #:use-module (gnu packages gl)
  54   #:use-module (gnu packages m4)
  55   #:use-module (gnu packages mpi)
  56   #:use-module (gnu packages multiprecision)
  57   #:use-module (gnu packages pcre)
  58   #:use-module (gnu packages popt)
  59   #:use-module (gnu packages perl)
  60   #:use-module (gnu packages pkg-config)
  61   #:use-module (gnu packages python)
  62   #:use-module (gnu packages readline)
  63   #:use-module (gnu packages tcsh)
  64   #:use-module (gnu packages tcl)
  65   #:use-module (gnu packages texinfo)
  66   #:use-module (gnu packages texlive)
  67   #:use-module (gnu packages xml))
  68
  69 (define-public units
  70   (package
  71    (name "units")
  72    (version "2.11")
  73    (source (origin
  74             (method url-fetch)
  75             (uri (string-append "mirror://gnu/units/units-" version
  76                                 ".tar.gz"))
  77             (sha256 (base32
  78                      "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
  79    (build-system gnu-build-system)
  80    (synopsis "Conversion between thousands of scales")
  81    (description
  82     "GNU Units converts numeric quantities between units of measure.  It
  83 can handle scale changes through adaptive usage of standard scale prefixes
  84 (micro-, kilo-, etc.).  It can also handle nonlinear conversions such as
  85 Fahrenheit to Celsius.  Its interpreter is powerful enough to be used
  86 effectively as a scientific calculator.")
  87    (license license:gpl3+)
  88    (home-page "http://www.gnu.org/software/units/")))
  89
  90 (define-public dionysus
  91   (package
  92     (name "dionysus")
  93     (version "1.3.0")
  94     (source (origin
  95               (method url-fetch)
  96               (uri (string-append "mirror://gnu/dionysus/dionysus-" version
  97                                   ".tar.gz"))
  98               (sha256
  99                (base32
 100                 "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
 101     (build-system gnu-build-system)
 102     (inputs `(("tcl" ,tcl)))                      ;for 'tclsh'
 103     (synopsis "Local search for universal constants and scientific values")
 104     (description
 105      "GNU Dionysus is a convenient system for quickly retrieving the values of
 106 mathematical constants used in science and engineering.  Values can be
 107 searched using a simple command-line tool, choosing from three databases:
 108 universal constants, atomic numbers, and constants related to
 109 semiconductors.")
 110     (license license:gpl3+)
 111     (home-page "http://www.gnu.org/software/dionysus/")))
 112
 113 (define-public gsl
 114   (package
 115     (name "gsl")
 116     (version "1.16")
 117     (source
 118      (origin
 119       (method url-fetch)
 120       (uri (string-append "mirror://gnu/gsl/gsl-"
 121                           version ".tar.gz"))
 122       (sha256
 123        (base32
 124         "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
 125     (build-system gnu-build-system)
 126     (arguments
 127      `(#:parallel-tests? #f
 128        #:phases
 129         (alist-replace
 130          'configure
 131          (lambda* (#:key target system outputs #:allow-other-keys #:rest args)
 132            (let ((configure (assoc-ref %standard-phases 'configure)))
 133              ;; disable numerically unstable test on i686, see thread at
 134              ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
 135              (if (string=? (or target system) "i686-linux")
 136                  (substitute* "ode-initval2/Makefile.in"
 137                    (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
 138              (apply configure args)))
 139          %standard-phases)))
 140     (home-page "http://www.gnu.org/software/gsl/")
 141     (synopsis "Numerical library for C and C++")
 142     (description
 143      "The GNU Scientific Library is a library for numerical analysis in C
 144 and C++.  It includes a wide range of mathematical routines, with over 1000
 145 functions in total.  Subject areas covered by the library include:
 146 differential equations, linear algebra, Fast Fourier Transforms and random
 147 numbers.")
 148     (license license:gpl3+)))
 149
 150 (define-public glpk
 151   (package
 152     (name "glpk")
 153     (version "4.55")
 154     (source
 155      (origin
 156       (method url-fetch)
 157       (uri (string-append "mirror://gnu/glpk/glpk-"
 158                           version ".tar.gz"))
 159       (sha256
 160        (base32
 161         "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
 162     (build-system gnu-build-system)
 163     (inputs
 164      `(("gmp" ,gmp)))
 165     (arguments
 166      `(#:configure-flags '("--with-gmp")))
 167     (home-page "http://www.gnu.org/software/glpk/")
 168     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 169     (description
 170      "GLPK is a C library for solving large-scale linear programming (LP),
 171 mixed integer programming (MIP), and other related problems.  It supports the
 172 GNU MathProg modeling language, a subset of the AMPL language, and features a
 173 translator for the language.  In addition to the C library, a stand-alone
 174 LP/MIP solver is included in the package.")
 175     (license license:gpl3+)))
 176
 177 (define-public pspp
 178   (package
 179     (name "pspp")
 180     (version "0.8.4")
 181     (source
 182      (origin
 183       (method url-fetch)
 184       (uri (string-append "mirror://gnu/pspp/pspp-"
 185                           version ".tar.gz"))
 186       (sha256
 187        (base32
 188         "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
 189     (build-system gnu-build-system)
 190     (inputs
 191      `(("cairo" ,cairo)
 192        ("fontconfig" ,fontconfig)
 193        ("gettext" ,gnu-gettext)
 194        ("gsl" ,gsl)
 195        ("libxml2" ,libxml2)
 196        ("pango" ,pango)
 197        ("readline" ,readline)
 198        ("gtk" ,gtk+-2)
 199        ("gtksourceview" ,gtksourceview)
 200        ("zlib" ,zlib)))
 201     (native-inputs
 202      `(("glib" ,glib "bin")             ;for glib-genmarshal
 203        ("perl" ,perl)
 204        ("pkg-config" ,pkg-config)))
 205     (home-page "http://www.gnu.org/software/pspp/")
 206     (synopsis "Statistical analysis")
 207     (description
 208      "GNU PSPP is a statistical analysis program.  It can perform
 209 descriptive statistics, T-tests, linear regression and non-parametric tests.
 210 It features both a graphical interface as well as command-line input.  PSPP
 211 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice.  Data
 212 can be imported from spreadsheets, text files and database sources and it can
 213 be output in text, PostScript, PDF or HTML.")
 214     (license license:gpl3+)))
 215
 216 (define-public arpack-ng
 217   (package
 218     (name "arpack-ng")
 219     (version "3.2.0")
 220     (source
 221      (origin
 222        (method url-fetch)
 223        (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
 224                            version ".tar.gz"))
 225        (file-name (string-append name "-" version ".tar.gz"))
 226        (sha256
 227         (base32
 228          "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
 229     (build-system gnu-build-system)
 230     (home-page "https://github.com/opencollab/arpack-ng")
 231     (inputs
 232      `(("lapack" ,lapack)
 233        ("fortran" ,gfortran-4.8)))
 234     (synopsis "Fortran subroutines for solving eigenvalue problems")
 235     (description
 236      "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
 237 large scale eigenvalue problems.")
 238     (license (license:bsd-style "file://COPYING"
 239                                 "See COPYING in the distribution."))))
 240
 241 (define-public lapack
 242   (package
 243     (name "lapack")
 244     (version "3.5.0")
 245     (source
 246      (origin
 247       (method url-fetch)
 248       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 249                           version ".tgz"))
 250       (sha256
 251        (base32
 252         "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
 253     (build-system cmake-build-system)
 254     (home-page "http://www.netlib.org/lapack/")
 255     (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
 256     (inputs `(("fortran" ,gfortran-4.8)
 257               ("python" ,python-2)))
 258     (arguments
 259      `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
 260        #:phases (alist-cons-before
 261                  'check 'patch-python
 262                  (lambda* (#:key inputs #:allow-other-keys)
 263                    (let ((python (assoc-ref inputs "python")))
 264                      (substitute* "lapack_testing.py"
 265                        (("/usr/bin/env python") python))))
 266                   %standard-phases)))
 267     (synopsis "Library for numerical linear algebra")
 268     (description
 269      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 270 problems in numerical linear algebra.")
 271     (license (license:bsd-style "file://LICENSE"
 272                                 "See LICENSE in the distribution."))))
 273
 274 (define-public gnuplot
 275   (package
 276     (name "gnuplot")
 277     (version "4.6.3")
 278     (source
 279      (origin
 280       (method url-fetch)
 281       (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
 282                                 version "/gnuplot-" version ".tar.gz"))
 283       (sha256
 284        (base32
 285         "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
 286     (build-system gnu-build-system)
 287     (inputs `(("readline" ,readline)
 288               ("cairo" ,cairo)
 289               ("pango" ,pango)
 290               ("gd" ,gd)))
 291     (native-inputs `(("texlive" ,texlive)
 292                      ("pkg-config" ,pkg-config)))
 293     (home-page "http://www.gnuplot.info")
 294     (synopsis "Command-line driven graphing utility")
 295     (description "Gnuplot is a portable command-line driven graphing
 296 utility.  It was originally created to allow scientists and students to
 297 visualize mathematical functions and data interactively, but has grown to
 298 support many non-interactive uses such as web scripting.  It is also used as a
 299 plotting engine by third-party applications like Octave.")
 300     ;;  X11 Style with the additional restriction that derived works may only be
 301     ;;  distributed as patches to the original.
 302     (license (license:fsf-free
 303               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
 304
 305 (define-public hdf5
 306   (package
 307     (name "hdf5")
 308     (version "1.8.12")
 309     (source
 310      (origin
 311       (method url-fetch)
 312       (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-"
 313                           version "/src/hdf5-"
 314                           version ".tar.bz2"))
 315       (sha256
 316        (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
 317     (build-system gnu-build-system)
 318     (arguments
 319      `(#:phases
 320         (alist-cons-before
 321          'configure 'patch-configure
 322          (lambda _
 323            (substitute* "configure"
 324              (("/bin/mv") "mv")))
 325          %standard-phases)))
 326     (outputs '("out" "bin" "lib" "include"))
 327     (home-page "http://www.hdfgroup.org")
 328     (synopsis "Management suite for extremely large and complex data")
 329     (description "HDF5 is a suite that makes possible the management of
 330 extremely large and complex data collections.")
 331     (license (license:x11-style
 332               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 333
 334
 335 ;; For a fully featured Octave, users  are strongly recommended also to install
 336 ;; the following packages: texinfo, less, ghostscript, gnuplot.
 337 (define-public octave
 338   (package
 339     (name "octave")
 340     (version "3.8.0")
 341     (source
 342      (origin
 343       (method url-fetch)
 344       (uri (string-append "mirror://gnu/octave/octave-"
 345                           version ".tar.gz"))
 346       (sha256
 347        (base32
 348         "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
 349     (build-system gnu-build-system)
 350     (inputs
 351      `(("lapack" ,lapack)
 352        ("readline" ,readline)
 353        ("glpk" ,glpk)
 354        ("curl" ,curl)
 355        ("pcre" ,pcre)
 356        ("fltk" ,fltk)
 357        ("fontconfig" ,fontconfig)
 358        ("freetype" ,freetype)
 359        ("hdf5-lib" ,hdf5 "lib")
 360        ("hdf5-include" ,hdf5 "include")
 361        ("libxft" ,libxft)
 362        ("mesa" ,mesa)
 363        ("zlib" ,zlib)))
 364     (native-inputs
 365      `(("gfortran" ,gfortran-4.8)
 366        ("pkg-config" ,pkg-config)
 367        ("perl" ,perl)
 368        ;; The following inputs are not actually used in the build process.  However, the
 369        ;; ./configure gratuitously tests for their existence and assumes that programs not
 370        ;; present at build time are also not, and can never be, available at run time!
 371        ;; If these inputs are therefore not present, support for them will be built out.
 372        ;; However, Octave will still run without them, albeit without the features they
 373        ;; provide.
 374        ("less" ,less)
 375        ("texinfo" ,texinfo)
 376        ("ghostscript" ,ghostscript)
 377        ("gnuplot" ,gnuplot)))
 378     (arguments
 379      `(#:configure-flags (list (string-append "--with-shell="
 380                             (assoc-ref %build-inputs "bash")
 381                             "/bin/sh"))))
 382     (home-page "http://www.gnu.org/software/octave/")
 383     (synopsis "High-level language for numerical computation")
 384     (description "GNU Octave is a high-level interpreted language that is specialized
 385 for numerical computations.  It can be used for both linear and non-linear
 386 applications and it provides great support for visualizing results.  Work may
 387 be performed both at the interactive command-line as well as via script
 388 files.")
 389     (license license:gpl3+)))
 390
 391 (define-public gmsh
 392   (package
 393     (name "gmsh")
 394     (version "2.8.4")
 395     (source
 396      (origin
 397       (method url-fetch)
 398       (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
 399                           version "-source.tgz"))
 400       (sha256
 401        (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
 402       (modules '((guix build utils)))
 403       (snippet
 404        ;; Remove non-free METIS code
 405        '(delete-file-recursively "contrib/Metis"))))
 406     (build-system cmake-build-system)
 407     (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
 408     (propagated-inputs
 409      `(("fltk" ,fltk)
 410        ("gfortran" ,gfortran-4.8)
 411        ("gmp" ,gmp)
 412        ("hdf5-lib" ,hdf5 "lib")
 413        ("hdf5-include" ,hdf5 "include")
 414        ("lapack" ,lapack)
 415        ("mesa" ,mesa)
 416        ("glu" ,glu)
 417        ("libx11" ,libx11)
 418        ("libxext" ,libxext)))
 419     (arguments
 420      `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
 421                            "-DENABLE_BUILD_SHARED:BOOL=ON"
 422                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
 423     (home-page "http://www.geuz.org/gmsh/")
 424     (synopsis "3D finite element grid generator")
 425     (description "Gmsh is a 3D finite element grid generator with a built-in
 426 CAD engine and post-processor.  Its design goal is to provide a fast, light
 427 and user-friendly meshing tool with parametric input and advanced
 428 visualization capabilities.  Gmsh is built around four modules: geometry,
 429 mesh, solver and post-processing.  The specification of any input to these
 430 modules is done either interactively using the graphical user interface or in
 431 ASCII text files using Gmsh's own scripting language.")
 432     (license license:gpl2+)))
 433
 434 (define-public petsc
 435   (package
 436     (name "petsc")
 437     (version "3.4.4")
 438     (source
 439      (origin
 440       (method url-fetch)
 441       ;; The *-lite-* tarball does not contain the *large* documentation
 442       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
 443                           "petsc-lite-" version ".tar.gz"))
 444       (sha256
 445        (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
 446       (patches
 447        (list (search-patch "petsc-fix-threadcomm.patch")))))
 448     (build-system gnu-build-system)
 449     (native-inputs
 450      `(("python" ,python-2)
 451        ("perl" ,perl)))
 452     (inputs
 453      `(("gfortran" ,gfortran-4.8)
 454        ("lapack" ,lapack)
 455        ("superlu" ,superlu)
 456        ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
 457        ;; leaving out opengl, as configuration seems to only be for mac
 458        ))
 459     (arguments
 460      `(#:test-target "test"
 461        #:parallel-build? #f
 462        #:configure-flags
 463        `("--with-mpi=0"
 464          "--with-openmp=1"
 465          "--with-superlu=1"
 466          ,(string-append "--with-superlu-include="
 467                          (assoc-ref %build-inputs "superlu") "/include")
 468          ,(string-append "--with-superlu-lib="
 469                          (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
 470        #:phases
 471        (alist-replace
 472         'configure
 473         ;; PETSc's configure script is actually a python script, so we can't
 474         ;; run it with bash.
 475         (lambda* (#:key outputs (configure-flags '())
 476                   #:allow-other-keys)
 477           (let* ((prefix (assoc-ref outputs "out"))
 478                  (flags `(,(string-append "--prefix=" prefix)
 479                           ,@configure-flags)))
 480             (format #t "build directory: ~s~%" (getcwd))
 481             (format #t "configure flags: ~s~%" flags)
 482             (zero? (apply system* "./configure" flags))))
 483         (alist-cons-after
 484          'configure 'clean-local-references
 485          ;; Try to keep build directory names from leaking into compiled code
 486          (lambda* (#:key inputs outputs #:allow-other-keys)
 487            (let ((out (assoc-ref outputs "out")))
 488              (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
 489                (((getcwd)) out))))
 490          (alist-cons-after
 491           'install 'clean-install
 492           ;; Try to keep installed files from leaking build directory names.
 493           (lambda* (#:key inputs outputs #:allow-other-keys)
 494             (let ((out     (assoc-ref outputs "out"))
 495                   (fortran (assoc-ref inputs  "gfortran")))
 496               (substitute* (map (lambda (file)
 497                                   (string-append out "/" file))
 498                                 '("conf/petscvariables"
 499                                   "conf/PETScConfig.cmake"))
 500                 (((getcwd)) out))
 501               ;; Make compiler references point to the store
 502               (substitute* (string-append out "/conf/petscvariables")
 503                 (("= g(cc|\\+\\+|fortran)" _ suffix)
 504                  (string-append "= " fortran "/bin/g" suffix)))
 505               ;; PETSc installs some build logs, which aren't necessary.
 506               (for-each (lambda (file)
 507                           (let ((f (string-append out "/" file)))
 508                             (when (file-exists? f)
 509                               (delete-file f))))
 510                         '("conf/configure.log"
 511                           "conf/make.log"
 512                           "conf/test.log"
 513                           "conf/error.log"
 514                           "conf/RDict.db"
 515                           ;; Once installed, should uninstall with Guix
 516                           "conf/uninstall.py"))))
 517           %standard-phases)))))
 518     (home-page "http://www.mcs.anl.gov/petsc")
 519     (synopsis "Library to solve PDEs")
 520     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
 521 data structures and routines for the scalable (parallel) solution of
 522 scientific applications modeled by partial differential equations.")
 523     (license (license:bsd-style
 524               "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
 525
 526 (define-public petsc-complex
 527   (package (inherit petsc)
 528     (location (source-properties->location (current-source-location)))
 529     (name "petsc-complex")
 530     (arguments
 531      (substitute-keyword-arguments (package-arguments petsc)
 532        ((#:configure-flags cf)
 533         `(cons "--with-scalar-type=complex" ,cf))))
 534     (synopsis "Library to solve PDEs (with complex scalars)")))
 535
 536 (define-public petsc-openmpi
 537   (package (inherit petsc)
 538     (name "petsc-openmpi")
 539     (inputs
 540      `(("openmpi" ,openmpi)
 541        ,@(package-inputs petsc)))
 542     (arguments
 543      (substitute-keyword-arguments (package-arguments petsc)
 544        ((#:configure-flags cf)
 545         ``("--with-mpiexec=mpirun"
 546            ,(string-append "--with-mpi-dir="
 547                            (assoc-ref %build-inputs "openmpi"))
 548            ,@(delete "--with-mpi=0" ,cf)))))
 549     (synopsis "Library to solve PDEs (with MPI support)")))
 550
 551 (define-public petsc-complex-openmpi
 552   (package (inherit petsc-complex)
 553     (name "petsc-complex-openmpi")
 554     (inputs
 555      `(("openmpi" ,openmpi)
 556        ,@(package-inputs petsc-complex)))
 557     (arguments
 558      (substitute-keyword-arguments (package-arguments petsc-complex)
 559        ((#:configure-flags cf)
 560         ``("--with-mpiexec=mpirun"
 561            ,(string-append "--with-mpi-dir="
 562                            (assoc-ref %build-inputs "openmpi"))
 563            ,@(delete "--with-mpi=0" ,cf)))))
 564     (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
 565
 566 (define-public superlu
 567   (package
 568     (name "superlu")
 569     (version "4.3")
 570     (source
 571      (origin
 572        (method url-fetch)
 573        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
 574                            "superlu_" version ".tar.gz"))
 575        (sha256
 576         (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n"))))
 577     (build-system gnu-build-system)
 578     (native-inputs
 579      `(("tcsh" ,tcsh)))
 580     (inputs
 581      `(("lapack" ,lapack)
 582        ("gfortran" ,gfortran-4.8)))
 583     (arguments
 584      `(#:parallel-build? #f
 585        #:tests? #f                      ;tests are run as part of `make all`
 586        #:phases
 587        (alist-replace
 588         'configure
 589         (lambda* (#:key inputs outputs #:allow-other-keys)
 590           (call-with-output-file "make.inc"
 591             (lambda (port)
 592               (format port "
 593 PLAT        =
 594 SuperLUroot = ~a
 595 SUPERLULIB  = ~a/lib/libsuperlu.a
 596 TMGLIB      = libtmglib.a
 597 BLASDEF     = -DUSE_VENDOR_BLAS
 598 BLASLIB     = -L~a/lib -lblas
 599 LIBS        = $(SUPERLULIB) $(BLASLIB)
 600 ARCH        = ar
 601 ARCHFLAGS   = cr
 602 RANLIB      = ranlib
 603 CC          = gcc
 604 PIC         = -fPIC
 605 CFLAGS      = -O3 -DPRNTlevel=0 $(PIC)
 606 NOOPTS      = -O0 $(PIC)
 607 FORTRAN     = gfortran
 608 FFLAGS      = -O2 $(PIC)
 609 LOADER      = $(CC)
 610 CDEFS       = -DAdd_"
 611                       (getcwd)
 612                       (assoc-ref outputs "out")
 613                       (assoc-ref inputs "lapack")))))
 614         (alist-cons-before
 615          'build 'create-install-directories
 616          (lambda* (#:key outputs #:allow-other-keys)
 617            (for-each
 618             (lambda (dir)
 619               (mkdir-p (string-append (assoc-ref outputs "out")
 620                                       "/" dir)))
 621             '("lib" "include")))
 622          (alist-replace
 623           'install
 624           (lambda* (#:key outputs #:allow-other-keys)
 625             ;; Library is placed in lib during the build phase.  Copy over
 626             ;; headers to include.
 627             (let* ((out    (assoc-ref outputs "out"))
 628                    (incdir (string-append out "/include")))
 629               (for-each (lambda (file)
 630                           (let ((base (basename file)))
 631                             (format #t "installing `~a' to `~a'~%"
 632                                     base incdir)
 633                             (copy-file file
 634                                        (string-append incdir "/" base))))
 635                         (find-files "SRC" ".*\\.h$"))))
 636           %standard-phases)))))
 637     (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
 638     (synopsis "Supernodal direct solver for sparse linear systems")
 639     (description
 640      "SuperLU is a general purpose library for the direct solution of large,
 641 sparse, nonsymmetric systems of linear equations on high performance machines.
 642 The library is written in C and is callable from either C or Fortran.  The
 643 library routines perform an LU decomposition with partial pivoting and
 644 triangular system solves through forward and back substitution.  The library
 645 also provides threshold-based ILU factorization preconditioners.")
 646     (license license:bsd-3)))
 647
 648 (define-public superlu-dist
 649   (package
 650     (name "superlu-dist")
 651     (version "3.3")
 652     (source
 653      (origin
 654        (method url-fetch)
 655        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
 656                            "superlu_dist_" version ".tar.gz"))
 657        (sha256
 658         (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
 659        (patches (list (search-patch "superlu-dist-scotchmetis.patch")))))
 660     (build-system gnu-build-system)
 661     (native-inputs
 662      `(("tcsh" ,tcsh)))
 663     (inputs
 664      `(("gfortran" ,gfortran-4.8)))
 665     (propagated-inputs
 666      `(("openmpi" ,openmpi)             ;headers include MPI heades
 667        ("lapack" ,lapack)               ;required to link with output library
 668        ("pt-scotch" ,pt-scotch)))       ;same
 669     (arguments
 670      `(#:parallel-build? #f             ;race conditions using ar
 671        #:phases
 672        (alist-replace
 673         'configure
 674         (lambda* (#:key inputs outputs #:allow-other-keys)
 675           (call-with-output-file "make.inc"
 676             (lambda (port)
 677               (format port "
 678 PLAT        =
 679 DSuperLUroot = ~a
 680 DSUPERLULIB  = ~a/lib/libsuperlu_dist.a
 681 BLASDEF     = -DUSE_VENDOR_BLAS
 682 BLASLIB     = -L~a/lib -lblas
 683 PARMETISLIB = -L~a/lib \
 684               -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
 685               -lscotch -lscotcherr -lscotcherrexit
 686 METISLIB    = -L~:*~a/lib \
 687               -lscotchmetis -lscotch -lscotcherr -lscotcherrexit
 688 LIBS        = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
 689 ARCH        = ar
 690 ARCHFLAGS   = cr
 691 RANLIB      = ranlib
 692 CC          = mpicc
 693 PIC         = -fPIC
 694 CFLAGS      = -O3 -g -DPRNTlevel=0 $(PIC)
 695 NOOPTS      = -O0 -g $(PIC)
 696 FORTRAN     = mpifort
 697 FFLAGS      = -O2 -g $(PIC)
 698 LOADER      = $(CC)
 699 CDEFS       = -DAdd_"
 700                       (getcwd)
 701                       (assoc-ref outputs "out")
 702                       (assoc-ref inputs "lapack")
 703                       (assoc-ref inputs "pt-scotch")))))
 704         (alist-cons-after
 705          'unpack 'remove-broken-symlinks
 706          (lambda _
 707            (for-each delete-file
 708                      (find-files "MAKE_INC" "\\.#make\\..*")))
 709          (alist-cons-before
 710           'build 'create-install-directories
 711           (lambda* (#:key outputs #:allow-other-keys)
 712             (for-each
 713              (lambda (dir)
 714                (mkdir-p (string-append (assoc-ref outputs "out")
 715                                        "/" dir)))
 716              '("lib" "include")))
 717           (alist-replace
 718            'check
 719            (lambda _
 720              (with-directory-excursion "EXAMPLE"
 721                (and
 722                 (zero? (system* "mpirun" "-n" "2"
 723                                 "./pddrive" "-r" "1" "-c" "2" "g20.rua"))
 724                 (zero? (system* "mpirun" "-n" "2"
 725                                 "./pzdrive" "-r" "1" "-c" "2" "cg20.cua")))))
 726            (alist-replace
 727             'install
 728             (lambda* (#:key outputs #:allow-other-keys)
 729               ;; Library is placed in lib during the build phase.  Copy over
 730               ;; headers to include.
 731               (let* ((out    (assoc-ref outputs "out"))
 732                      (incdir (string-append out "/include")))
 733                 (for-each (lambda (file)
 734                             (let ((base (basename file)))
 735                               (format #t "installing `~a' to `~a'~%"
 736                                       base incdir)
 737                               (copy-file file
 738                                          (string-append incdir "/" base))))
 739                           (find-files "SRC" ".*\\.h$"))))
 740             %standard-phases)))))))
 741     (home-page (package-home-page superlu))
 742     (synopsis "Parallel supernodal direct solver")
 743     (description
 744      "SuperLU_DIST is a parallel extension to the serial SuperLU library.
 745 It is targeted for distributed memory parallel machines.  SuperLU_DIST is
 746 implemented in ANSI C, and MPI for communications.")
 747     (license license:bsd-3)))
 748
 749 (define-public scotch
 750   (package
 751     (name "scotch")
 752     (version "6.0.0")
 753     (source
 754      (origin
 755       (method url-fetch)
 756       (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/"
 757                           "scotch_" version ".tar.gz"))
 758       (sha256
 759        (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
 760       (patches (list (search-patch "scotch-test-threading.patch")))))
 761     (build-system gnu-build-system)
 762     (inputs
 763      `(("zlib" ,zlib)
 764        ("flex" ,flex)
 765        ("bison" ,bison)))
 766     (arguments
 767      `(#:phases
 768        (alist-cons-after
 769         'unpack 'chdir-to-src
 770         (lambda _ (chdir "src"))
 771         (alist-replace
 772          'configure
 773          (lambda _
 774            (call-with-output-file "Makefile.inc"
 775              (lambda (port)
 776                (format port "
 777 EXE =
 778 LIB = .a
 779 OBJ = .o
 780 MAKE = make
 781 AR = ar
 782 ARFLAGS = -ruv
 783 CCS = gcc
 784 CCP = mpicc
 785 CCD = gcc
 786 CPPFLAGS =~{ -D~a~}
 787 CFLAGS = -O2 -g $(CPPFLAGS)
 788 LDFLAGS = -lz -lm -lrt -lpthread
 789 CP = cp
 790 LEX = flex -Pscotchyy -olex.yy.c
 791 LN = ln
 792 MKDIR = mkdir
 793 MV = mv
 794 RANLIB = ranlib
 795 YACC = bison -pscotchyy -y -b y
 796 "
 797                        '("COMMON_FILE_COMPRESS_GZ"
 798                          "COMMON_PTHREAD"
 799                          "COMMON_RANDOM_FIXED_SEED"
 800                          ;; TODO: Define once our MPI supports
 801                          ;; MPI_THREAD_MULTIPLE
 802                          ;; "SCOTCH_PTHREAD"
 803                          ;; "SCOTCH_PTHREAD_NUMBER=2"
 804                          "restrict=__restrict")))))
 805          (alist-replace
 806           'install
 807           (lambda* (#:key outputs #:allow-other-keys)
 808             (let ((out (assoc-ref outputs "out")))
 809               (mkdir out)
 810               (zero? (system* "make"
 811                               (string-append "prefix=" out)
 812                               "install"))))
 813           %standard-phases)))))
 814     (home-page "http://www.labri.fr/perso/pelegrin/scotch/")
 815     (synopsis "Programs and libraries for graph algorithms")
 816     (description "SCOTCH is a set of programs and libraries which implement
 817 the static mapping and sparse matrix reordering algorithms developed within
 818 the SCOTCH project.  Its purpose is to apply graph theory, with a divide and
 819 conquer approach, to scientific computing problems such as graph and mesh
 820 partitioning, static mapping, and sparse matrix ordering, in application
 821 domains ranging from structural mechanics to operating systems or
 822 bio-chemistry.")
 823     ;; See LICENSE_en.txt
 824     (license license:cecill-c)))
 825
 826 (define-public pt-scotch
 827   (package (inherit scotch)
 828     (name "pt-scotch")
 829     (propagated-inputs
 830      `(("openmpi" ,openmpi)))           ;Headers include MPI headers
 831     (arguments
 832      (substitute-keyword-arguments (package-arguments scotch)
 833        ((#:phases scotch-phases)
 834         `(alist-replace
 835           'build
 836           ;; TODO: Would like to add parallelism here
 837           (lambda _
 838             (and
 839              (zero? (system* "make" "ptscotch"))
 840              ;; Install the serial metis compatibility library
 841              (zero? (system* "make" "-C" "libscotchmetis" "install"))))
 842           (alist-replace
 843            'check
 844            (lambda _ (zero? (system* "make" "ptcheck")))
 845            (alist-replace
 846             'install
 847             (lambda* (#:key outputs #:allow-other-keys)
 848               (let ((out (assoc-ref outputs "out")))
 849                 (mkdir out)
 850                 (zero? (system* "make"
 851                                 (string-append "prefix=" out)
 852                                 "install"))))
 853             ,scotch-phases))))))
 854     (synopsis "Programs and libraries for graph algorithms (with MPI)")))
 855
 856 (define-public gsegrafix
 857   (package
 858     (name "gsegrafix")
 859     (version "1.0.6")
 860     (source
 861      (origin
 862       (method url-fetch)
 863       (uri (string-append "mirror://gnu/" name "/" name "-"
 864                           version ".tar.gz"))
 865       (sha256
 866        (base32
 867         "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda"))))
 868     (build-system gnu-build-system)
 869     (arguments
 870      `(#:configure-flags '("LDFLAGS=-lm")))
 871     (inputs
 872      `(("libgnomecanvas" ,libgnomecanvas)
 873        ("libbonoboui" ,libbonoboui)
 874        ("libgnomeui" ,libgnomeui)
 875        ("libgnomeprintui" ,libgnomeprintui)
 876        ("popt" ,popt)))
 877     (native-inputs
 878      `(("pkg-config" ,pkg-config)))
 879     (home-page "http://www.gnu.org/software/gsegrafix/")
 880     (synopsis "GNOME application to create scientific and engineering plots")
 881     (description  "GSEGrafix is an application which produces high-quality graphical
 882 plots for science and engineering.  Plots are specified via simple ASCII
 883 parameter files and data files and are presented in an anti-aliased GNOME
 884 canvas.  The program supports rectangular two-dimensional plots, histograms,
 885 polar-axis plots and three-dimensional plots.  Plots can be printed or saved
 886 to BMP, JPEG or PNG image formats.")
 887     (license license:gpl3+)))
 888
 889 (define-public maxima
 890   (package
 891     (name "maxima")
 892     (version "5.34.1")
 893     (source
 894      (origin
 895        (method url-fetch)
 896        (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
 897                            version "-source/" name "-" version ".tar.gz"))
 898        (sha256
 899         (base32
 900          "1dw9vfzldpj7lv303xbw0wpyn6ra6i2yzwlrjbcx7j0jm5n43ji0"))))
 901     (build-system gnu-build-system)
 902     (inputs
 903      `(("gcl" ,gcl)
 904        ("gnuplot" ,gnuplot)                       ;for plots
 905        ("tk" ,tk)))                               ;Tcl/Tk is used by 'xmaxima'
 906     (native-inputs
 907      `(("texinfo" ,texinfo)
 908        ("perl" ,perl)))
 909     (arguments
 910      `(#:configure-flags
 911        (list "--enable-gcl"
 912              (string-append "--with-posix-shell="
 913                             (assoc-ref %build-inputs "bash")
 914                             "/bin/sh")
 915              (string-append "--with-wish="
 916                             (assoc-ref %build-inputs "tk")
 917                             "/bin/wish"
 918                             (let ((v ,(package-version tk)))
 919                               (string-take v (string-index-right v #\.)))))
 920        ;; By default Maxima attempts to write temporary files to
 921        ;; '/tmp/nix-build-maxima-5.34.1', which doesn't exist.  Work around
 922        ;; that.
 923        #:make-flags (list "TMPDIR=/tmp")
 924        #:phases (alist-cons-before
 925                  'check 'pre-check
 926                  (lambda _
 927                    (chmod "src/maxima" #o555))
 928                  ;; Make sure the doc and emacs files are found in the
 929                  ;; standard location.  Also configure maxima to find gnuplot
 930                  ;; without having it on the PATH.
 931                  (alist-cons-after
 932                   'install 'post-install
 933                   (lambda* (#:key outputs inputs #:allow-other-keys)
 934                     (let* ((gnuplot (assoc-ref inputs "gnuplot"))
 935                           (out (assoc-ref outputs "out"))
 936                           (datadir (string-append out "/share/maxima/" ,version)))
 937                       (with-directory-excursion out
 938                         (mkdir-p "share/emacs")
 939                         (mkdir-p "share/doc")
 940                         (symlink
 941                          (string-append datadir "/emacs/")
 942                          (string-append out "/share/emacs/site-lisp"))
 943                         (symlink
 944                          (string-append datadir "/doc/")
 945                          (string-append out "/share/doc/maxima"))
 946                         (with-atomic-file-replacement
 947                          (string-append datadir "/share/maxima-init.lisp")
 948                          (lambda (in out)
 949                            (format out "~a ~s~a~%"
 950                                    "(setf $gnuplot_command "
 951                                    (string-append gnuplot "/bin/gnuplot") ")")
 952                            (dump-port in out))))))
 953                   %standard-phases))))
 954     (home-page "http://maxima.sourceforge.net")
 955     (synopsis "Numeric and symbolic expression manipulation")
 956     (description "Maxima is a system for the manipulation of symbolic and
 957 numerical expressions.  It yields high precision numeric results by using
 958 exact fractions, arbitrary precision integers, and variable precision floating
 959 point numbers")
 960     ;; Some files are lgpl2.1+. Some are gpl2+.  Some explicitly state gpl1+.
 961     ;; Others simply say "GNU General Public License" without stating a
 962     ;; version (which implicitly means gpl1+).
 963     ;; At least one file (src/maxima.asd) says "version 2."
 964     ;; GPLv2 only is therefore the smallest subset.
 965     (license license:gpl2)))
 966
 967 (define-public atlas
 968   (package
 969     (name "atlas")
 970     (version "3.10.2")
 971     (source (origin
 972               (method url-fetch)
 973               (uri (string-append "mirror://sourceforge/math-atlas/atlas"
 974                                   version ".tar.bz2"))
 975               (sha256
 976                (base32
 977                 "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars"))))
 978     (build-system gnu-build-system)
 979     (home-page "http://math-atlas.sourceforge.net/")
 980     (inputs `(("gfortran" ,gfortran-4.8)
 981               ("lapack-tar" ,(package-source lapack))))
 982     (outputs '("out" "doc"))
 983     ;; For the moment we drop support for MIPS at it fails to compile. See
 984     ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
 985     (supported-systems (delete "mips64el-linux" %supported-systems))
 986     (arguments
 987      `(#:parallel-build? #f
 988        #:parallel-tests? #f
 989
 990        ;; ATLAS tunes itself for the machine it is built on, as explained at
 991        ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
 992        ;; For this reason, we want users to build it locally instead of using
 993        ;; substitutes.
 994        #:substitutable? #f
 995
 996        #:modules ((srfi srfi-26)
 997                   (srfi srfi-1)
 998                   (guix build gnu-build-system)
 999                   (guix build utils))
1000        #:configure-flags
1001        `(;; Generate position independent code suitable for dynamic libraries
1002          ;; and use WALL timer to get more accurate timing.
1003          "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
1004          ;; Set word width.
1005          "-b"
1006          ,,(if (string-match "64" (%current-system))
1007                "64"
1008                "32")
1009          ;; Disable parallel build as it gives errors: atlas_pthread.h is
1010          ;; needed to compile C files before it is generated.
1011          "-Ss" "pmake" "make -j 1"
1012          ;; Probe is failing for MIPS.  We therefore define the system
1013          ;; architecture explicitly by setting (-A) MACHINETYPE = 49
1014          ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
1015          ,,@(if (string-prefix? "mips" (%current-system))
1016               (list "-A" "49" "-V" "1")
1017               (list))
1018          ;; Generate shared libraries.
1019          "--shared"
1020          ;; Build a full LAPACK library.
1021          ,(string-append "--with-netlib-lapack-tarfile="
1022                          (assoc-ref %build-inputs "lapack-tar")))
1023        #:phases
1024         (alist-cons-after
1025          'install 'install-doc
1026          (lambda* (#:key outputs inputs #:allow-other-keys)
1027            (let ((doc (string-append (assoc-ref outputs "doc")
1028                                      "/share/doc/atlas")))
1029              (mkdir-p doc)
1030              (fold (lambda (file previous)
1031                      (and previous (zero? (system* "cp" file doc))))
1032                    #t (find-files "../ATLAS/doc" ".*"))))
1033          (alist-cons-after
1034           'check 'check-pt
1035           (lambda _ (zero? (system* "make" "ptcheck")))
1036           ;; Fix files required to run configure.
1037           (alist-cons-before
1038            'configure 'fix-/bin/sh
1039            (lambda _
1040              ;; Use `sh', not `/bin/sh'.
1041              (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
1042                (("/bin/sh")
1043                 "sh")))
1044            ;; Fix /bin/sh in generated make files.
1045            (alist-cons-after
1046             'configure 'fix-/bin/sh-in-generated-files
1047             (lambda _
1048               (substitute* (find-files "." "^[Mm]ake\\.inc.*")
1049                 (("/bin/sh")
1050                  "sh")))
1051             ;; ATLAS configure program does not accepts the default flags
1052             ;; passed by the 'gnu-build-system'.
1053             (alist-replace
1054              'configure
1055              (lambda* (#:key native-inputs inputs outputs
1056                              (configure-flags '())
1057                              #:allow-other-keys #:rest args)
1058                (let* ((prefix     (assoc-ref outputs "out"))
1059                       (bash       (or (and=> (assoc-ref
1060                                               (or native-inputs inputs) "bash")
1061                                              (cut string-append <> "/bin/bash"))
1062                                       "/bin/sh"))
1063                       (flags      `(,(string-append "--prefix=" prefix)
1064                                     ,@configure-flags))
1065                       (abs-srcdir (getcwd))
1066                       (srcdir     (string-append "../" (basename abs-srcdir))))
1067                  (format #t "source directory: ~s (relative from build: ~s)~%"
1068                          abs-srcdir srcdir)
1069                  (mkdir "../build")
1070                  (chdir "../build")
1071                  (format #t "build directory: ~s~%" (getcwd))
1072                  (format #t "configure flags: ~s~%" flags)
1073                  (zero? (apply system* bash
1074                                (string-append srcdir "/configure")
1075                                flags))))
1076              %standard-phases)))))))
1077     (synopsis "Automatically Tuned Linear Algebra Software")
1078     (description
1079      "ATLAS is an automatically tuned linear algebra software library
1080 providing C and Fortran77 interfaces to a portably efficient BLAS
1081 implementation, as well as a few routines from LAPACK.
1082
1083 Optimization occurs at build time.  For this reason, the library is built on
1084 the machine where it is installed, without resorting to pre-built substitutes.
1085
1086 Before building the library, CPU throttling should be disabled.  This can be
1087 done in the BIOS, or, on GNU/Linux, with the following commands:
1088
1089 cpufreq-selector -g performance -c 0
1090 ...
1091 cpufreq-selector -g performance -c N-1
1092
1093 where N is the number of cores of your CPU.  Failure to do so will result in a
1094 library with poor performance.")
1095     (license license:bsd-3)))