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 ;;;
   7 ;;; This file is part of GNU Guix.
   8 ;;;
   9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  10 ;;; under the terms of the GNU General Public License as published by
  11 ;;; the Free Software Foundation; either version 3 of the License, or (at
  12 ;;; your option) any later version.
  13 ;;;
  14 ;;; GNU Guix is distributed in the hope that it will be useful, but
  15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  17 ;;; GNU General Public License for more details.
  18 ;;;
  19 ;;; You should have received a copy of the GNU General Public License
  20 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  21
  22 (define-module (gnu packages maths)
  23   #:use-module (gnu packages)
  24   #:use-module ((guix licenses)
  25                 #:renamer (symbol-prefix-proc 'license:))
  26   #:use-module (guix packages)
  27   #:use-module (guix download)
  28   #:use-module (guix utils)
  29   #:use-module (guix build-system cmake)
  30   #:use-module (guix build-system gnu)
  31   #:use-module (gnu packages algebra)
  32   #:use-module (gnu packages bison)
  33   #:use-module (gnu packages cmake)
  34   #:use-module (gnu packages compression)
  35   #:use-module (gnu packages curl)
  36   #:use-module (gnu packages elf)
  37   #:use-module (gnu packages flex)
  38   #:use-module (gnu packages fltk)
  39   #:use-module (gnu packages fontutils)
  40   #:use-module (gnu packages gettext)
  41   #:use-module (gnu packages gcc)
  42   #:use-module (gnu packages gd)
  43   #:use-module (gnu packages ghostscript)
  44   #:use-module (gnu packages gtk)
  45   #:use-module (gnu packages less)
  46   #:use-module (gnu packages xorg)
  47   #:use-module (gnu packages gl)
  48   #:use-module (gnu packages multiprecision)
  49   #:use-module (gnu packages pcre)
  50   #:use-module (gnu packages perl)
  51   #:use-module (gnu packages pkg-config)
  52   #:use-module (gnu packages python)
  53   #:use-module (gnu packages readline)
  54   #:use-module (gnu packages tcsh)
  55   #:use-module (gnu packages texinfo)
  56   #:use-module (gnu packages texlive)
  57   #:use-module (gnu packages xml))
  58
  59 (define-public units
  60   (package
  61    (name "units")
  62    (version "2.11")
  63    (source (origin
  64             (method url-fetch)
  65             (uri (string-append "mirror://gnu/units/units-" version
  66                                 ".tar.gz"))
  67             (sha256 (base32
  68                      "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
  69    (build-system gnu-build-system)
  70    (synopsis "Conversion between thousands of scales")
  71    (description
  72     "GNU Units converts numeric quantities between units of measure.  It
  73 can handle scale changes through adaptive usage of standard scale prefixes
  74 (micro-, kilo-, etc.).  It can also handle nonlinear conversions such as
  75 Fahrenheit to Celsius.  Its interpreter is powerful enough to be used
  76 effectively as a scientific calculator.")
  77    (license license:gpl3+)
  78    (home-page "http://www.gnu.org/software/units/")))
  79
  80 (define-public gsl
  81   (package
  82     (name "gsl")
  83     (version "1.16")
  84     (source
  85      (origin
  86       (method url-fetch)
  87       (uri (string-append "mirror://gnu/gsl/gsl-"
  88                           version ".tar.gz"))
  89       (sha256
  90        (base32
  91         "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
  92     (build-system gnu-build-system)
  93     (arguments
  94      `(#:parallel-tests? #f
  95        #:phases
  96         (alist-replace
  97          'configure
  98          (lambda* (#:key target system outputs #:allow-other-keys #:rest args)
  99            (let ((configure (assoc-ref %standard-phases 'configure)))
 100              ;; disable numerically unstable test on i686, see thread at
 101              ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
 102              (if (string=? (or target system) "i686-linux")
 103                  (substitute* "ode-initval2/Makefile.in"
 104                    (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
 105              (apply configure args)))
 106          %standard-phases)))
 107     (home-page "http://www.gnu.org/software/gsl/")
 108     (synopsis "Numerical library for C and C++")
 109     (description
 110      "The GNU Scientific Library is a library for numerical analysis in C
 111 and C++.  It includes a wide range of mathematical routines, with over 1000
 112 functions in total.  Subject areas covered by the library include:
 113 differential equations, linear algebra, Fast Fourier Transforms and random
 114 numbers.")
 115     (license license:gpl3+)))
 116
 117 (define-public glpk
 118   (package
 119     (name "glpk")
 120     (version "4.54")
 121     (source
 122      (origin
 123       (method url-fetch)
 124       (uri (string-append "mirror://gnu/glpk/glpk-"
 125                           version ".tar.gz"))
 126       (sha256
 127        (base32
 128         "18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb"))))
 129     (build-system gnu-build-system)
 130     (inputs
 131      `(("gmp" ,gmp)))
 132     (arguments
 133      `(#:configure-flags '("--with-gmp")))
 134     (home-page "http://www.gnu.org/software/glpk/")
 135     (synopsis "GNU Linear Programming Kit, supporting the MathProg language")
 136     (description
 137      "GLPK is a C library for solving large-scale linear programming (LP),
 138 mixed integer programming (MIP), and other related problems.  It supports the
 139 GNU MathProg modeling language, a subset of the AMPL language, and features a
 140 translator for the language.  In addition to the C library, a stand-alone
 141 LP/MIP solver is included in the package.")
 142     (license license:gpl3+)))
 143
 144 (define-public pspp
 145   (package
 146     (name "pspp")
 147     (version "0.8.2")
 148     (source
 149      (origin
 150       (method url-fetch)
 151       (uri (string-append "mirror://gnu/pspp/pspp-"
 152                           version ".tar.gz"))
 153       (sha256
 154        (base32
 155         "1w7h3dglgx0jlq1wb605b8pgfsk2vr1q2q2rj7bsajh9ihbcsixr"))))
 156     (build-system gnu-build-system)
 157     (inputs
 158      `(("cairo" ,cairo)
 159        ("fontconfig" ,fontconfig)
 160        ("gettext" ,gnu-gettext)
 161        ("gsl" ,gsl)
 162        ("libxml2" ,libxml2)
 163        ("pango" ,pango)
 164        ("readline" ,readline)
 165        ("gtk" ,gtk+-2)
 166        ("gtksourceview" ,gtksourceview)
 167        ("zlib" ,zlib)))
 168     (native-inputs
 169      `(("perl" ,perl)
 170        ("pkg-config" ,pkg-config)))
 171     (home-page "http://www.gnu.org/software/pspp/")
 172     (synopsis "Statistical analysis")
 173     (description
 174      "GNU PSPP is a statistical analysis program.  It can perform
 175 descriptive statistics, T-tests, linear regression and non-parametric tests.
 176 It features both a graphical interface as well as command-line input. PSPP is
 177 designed to interoperate with Gnumeric, LibreOffice and OpenOffice.  Data can
 178 be imported from spreadsheets, text files and database sources and it can be
 179 output in text, PostScript, PDF or HTML.")
 180     (license license:gpl3+)))
 181
 182 (define-public lapack
 183   (package
 184     (name "lapack")
 185     (version "3.5.0")
 186     (source
 187      (origin
 188       (method url-fetch)
 189       (uri (string-append "http://www.netlib.org/lapack/lapack-"
 190                           version ".tgz"))
 191       (sha256
 192        (base32
 193         "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
 194     (build-system cmake-build-system)
 195     (home-page "http://www.netlib.org/lapack/")
 196     (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
 197     (inputs `(("fortran" ,gfortran-4.8)
 198               ("python" ,python-2)))
 199     (arguments
 200      `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
 201        #:phases (alist-cons-before
 202                  'check 'patch-python
 203                  (lambda* (#:key inputs #:allow-other-keys)
 204                    (let ((python (assoc-ref inputs "python")))
 205                      (substitute* "lapack_testing.py"
 206                        (("/usr/bin/env python") python))))
 207                   %standard-phases)))
 208     (synopsis "Library for numerical linear algebra")
 209     (description
 210      "LAPACK is a Fortran 90 library for solving the most commonly occurring
 211 problems in numerical linear algebra.")
 212     (license (license:bsd-style "file://LICENSE"
 213                                 "See LICENSE in the distribution."))))
 214
 215 (define-public gnuplot
 216   (package
 217     (name "gnuplot")
 218     (version "4.6.3")
 219     (source
 220      (origin
 221       (method url-fetch)
 222       (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
 223                                 version "/gnuplot-" version ".tar.gz"))
 224       (sha256
 225        (base32
 226         "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
 227     (build-system gnu-build-system)
 228     (inputs `(("readline" ,readline)
 229               ("cairo" ,cairo)
 230               ("pango" ,pango)
 231               ("gd" ,gd)))
 232     (native-inputs `(("texlive" ,texlive)
 233                      ("pkg-config" ,pkg-config)))
 234     (home-page "http://www.gnuplot.info")
 235     (synopsis "Command-line driven graphing utility")
 236     (description "Gnuplot is a portable command-line driven graphing
 237 utility. It was originally created to allow scientists and students to
 238 visualize mathematical functions and data interactively, but has grown to
 239 support many non-interactive uses such as web scripting. It is also used as a
 240 plotting engine by third-party applications like Octave.")
 241     ;;  X11 Style with the additional restriction that derived works may only be
 242     ;;  distributed as patches to the original.
 243     (license (license:fsf-free
 244               "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
 245
 246 (define-public hdf5
 247   (package
 248     (name "hdf5")
 249     (version "1.8.12")
 250     (source
 251      (origin
 252       (method url-fetch)
 253       (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-"
 254                           version ".tar.bz2"))
 255       (sha256
 256        (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
 257     (build-system gnu-build-system)
 258     (arguments
 259      `(#:phases
 260         (alist-cons-before
 261          'configure 'patch-configure
 262          (lambda _
 263            (substitute* "configure"
 264              (("/bin/mv") "mv")))
 265          %standard-phases)))
 266     (outputs '("out" "bin" "lib" "include"))
 267     (home-page "http://www.hdfgroup.org")
 268     (synopsis "Management suite for  extremely large and complex data")
 269     (description "HDF5 is a suite that makes possible the management of
 270 extremely large and complex data collections.")
 271     (license (license:x11-style
 272               "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
 273
 274
 275 ;; For a fully featured Octave, users  are strongly recommended also to install
 276 ;; the following packages: texinfo, less, ghostscript, gnuplot.
 277 (define-public octave
 278   (package
 279     (name "octave")
 280     (version "3.8.0")
 281     (source
 282      (origin
 283       (method url-fetch)
 284       (uri (string-append "mirror://gnu/octave/octave-"
 285                           version ".tar.gz"))
 286       (sha256
 287        (base32
 288         "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
 289     (build-system gnu-build-system)
 290     (inputs
 291      `(("lapack" ,lapack)
 292        ("readline" ,readline)
 293        ("glpk" ,glpk)
 294        ("curl" ,curl)
 295        ("pcre" ,pcre)
 296        ("fltk" ,fltk)
 297        ("fontconfig" ,fontconfig)
 298        ("freetype" ,freetype)
 299        ("hdf5-lib" ,hdf5 "lib")
 300        ("hdf5-include" ,hdf5 "include")
 301        ("libxft" ,libxft)
 302        ("mesa" ,mesa)
 303        ("zlib" ,zlib)))
 304     (native-inputs
 305      `(("gfortran" ,gfortran-4.8)
 306        ("pkg-config" ,pkg-config)
 307        ("perl" ,perl)
 308        ;; The following inputs are not actually used in the build process.  However, the
 309        ;; ./configure gratuitously tests for their existence and assumes that programs not
 310        ;; present at build time are also not, and can never be, available at run time!
 311        ;; If these inputs are therefore not present, support for them will be built out.
 312        ;; However, Octave will still run without them, albeit without the features they
 313        ;; provide.
 314        ("less" ,less)
 315        ("texinfo" ,texinfo)
 316        ("ghostscript" ,ghostscript)
 317        ("gnuplot" ,gnuplot)))
 318     (arguments
 319      `(#:configure-flags (list (string-append "--with-shell="
 320                             (assoc-ref %build-inputs "bash")
 321                             "/bin/sh"))))
 322     (home-page "http://www.gnu.org/software/octave/")
 323     (synopsis "High-level language for numerical computation")
 324     (description "GNU Octave is a high-level interpreted language that is specialized
 325 for numerical computations.  It can be used for both linear and non-linear
 326 applications and it provides great support for visualizing results.  Work may
 327 be performed both at the interactive command-line as well as via script
 328 files.")
 329     (license license:gpl3+)))
 330
 331 (define-public gmsh
 332   (package
 333     (name "gmsh")
 334     (version "2.8.4")
 335     (source
 336      (origin
 337       (method url-fetch)
 338       (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
 339                           version "-source.tgz"))
 340       (sha256
 341        (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
 342       (modules '((guix build utils)))
 343       (snippet
 344        ;; Remove non-free METIS code
 345        '(delete-file-recursively "contrib/Metis"))))
 346     (build-system cmake-build-system)
 347     (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
 348     (propagated-inputs
 349      `(("fltk" ,fltk)
 350        ("gfortran" ,gfortran-4.8)
 351        ("gmp" ,gmp)
 352        ("hdf5-lib" ,hdf5 "lib")
 353        ("hdf5-include" ,hdf5 "include")
 354        ("lapack" ,lapack)
 355        ("mesa" ,mesa)
 356        ("libx11" ,libx11)
 357        ("libxext" ,libxext)))
 358     (arguments
 359      `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
 360                            "-DENABLE_BUILD_SHARED:BOOL=ON"
 361                            "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
 362     (home-page "http://www.geuz.org/gmsh/")
 363     (synopsis "3D finite element grid generator")
 364     (description "Gmsh is a 3D finite element grid generator with a built-in
 365 CAD engine and post-processor.  Its design goal is to provide a fast, light
 366 and user-friendly meshing tool with parametric input and advanced
 367 visualization capabilities.  Gmsh is built around four modules: geometry,
 368 mesh, solver and post-processing.  The specification of any input to these
 369 modules is done either interactively using the graphical user interface or in
 370 ASCII text files using Gmsh's own scripting language.")
 371     (license license:gpl2+)))
 372
 373 (define-public petsc
 374   (package
 375     (name "petsc")
 376     (version "3.4.4")
 377     (source
 378      (origin
 379       (method url-fetch)
 380       ;; The *-lite-* tarball does not contain the *large* documentation
 381       (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
 382                           "petsc-lite-" version ".tar.gz"))
 383       (sha256
 384        (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
 385       (patches
 386        (list (search-patch "petsc-fix-threadcomm.patch")))))
 387     (build-system gnu-build-system)
 388     (native-inputs
 389      `(("python" ,python-2)
 390        ("perl" ,perl)))
 391     (inputs
 392      `(("gfortran" ,gfortran-4.8)
 393        ("lapack" ,lapack)
 394        ("superlu" ,superlu)
 395        ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
 396        ;; leaving out opengl, as configuration seems to only be for mac
 397        ))
 398     (arguments
 399      `(#:test-target "test"
 400        #:parallel-build? #f
 401        #:configure-flags
 402        `("--with-mpi=0"
 403          "--with-openmp=1"
 404          "--with-superlu=1"
 405          ,(string-append "--with-superlu-include="
 406                          (assoc-ref %build-inputs "superlu") "/include")
 407          ,(string-append "--with-superlu-lib="
 408                          (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
 409        #:phases
 410        (alist-replace
 411         'configure
 412         ;; PETSc's configure script is actually a python script, so we can't
 413         ;; run it with bash.
 414         (lambda* (#:key outputs (configure-flags '())
 415                   #:allow-other-keys)
 416           (let* ((prefix (assoc-ref outputs "out"))
 417                  (flags `(,(string-append "--prefix=" prefix)
 418                           ,@configure-flags)))
 419             (format #t "build directory: ~s~%" (getcwd))
 420             (format #t "configure flags: ~s~%" flags)
 421             (zero? (apply system* "./configure" flags))))
 422         (alist-cons-after
 423          'install 'clean-local-references
 424          ;; Try to keep installed files from leaking build directory names.
 425          (lambda* (#:key inputs outputs #:allow-other-keys)
 426            (let ((out     (assoc-ref outputs "out"))
 427                  (fortran (assoc-ref inputs  "gfortran")))
 428              (substitute* (map (lambda (file)
 429                                  (string-append out "/" file))
 430                                '("conf/petscvariables"
 431                                  "conf/PETScConfig.cmake"
 432                                  "include/petscconf.h"
 433                                  "include/petscmachineinfo.h"))
 434                (((getcwd)) out))
 435              ;; Make compiler references point to the store
 436              (substitute* (string-append out "/conf/petscvariables")
 437                (("= g(cc|\\+\\+|fortran)" _ suffix)
 438                 (string-append "= " fortran "/bin/g" suffix)))
 439              ;; PETSc installs some build logs, which aren't necessary.
 440              (for-each (lambda (file)
 441                          (delete-file (string-append out "/" file)))
 442                        '("conf/configure.log"
 443                          "conf/make.log"
 444                          "conf/test.log"
 445                          "conf/RDict.db"
 446                          ;; Once installed, should uninstall with Guix
 447                          "conf/uninstall.py"))))
 448          %standard-phases))))
 449     (home-page "http://www.mcs.anl.gov/petsc")
 450     (synopsis "Library to solve ODEs and algebraic equations")
 451     (description "PETSc, pronounced PET-see (the S is silent), is a suite of
 452 data structures and routines for the scalable (parallel) solution of
 453 scientific applications modeled by partial differential equations.")
 454     (license (license:bsd-style
 455               "http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
 456
 457 (define-public petsc-complex
 458   (package (inherit petsc)
 459     (name "petsc-complex")
 460     (arguments
 461      (substitute-keyword-arguments (package-arguments petsc)
 462        ((#:configure-flags cf)
 463         `(cons "--with-scalar-type=complex" ,cf))))
 464     (description
 465      (string-append (package-description petsc)
 466                     "  Complex scalar type version."))))
 467
 468 (define-public superlu
 469   (package
 470     (name "superlu")
 471     (version "4.3")
 472     (source
 473      (origin
 474        (method url-fetch)
 475        (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
 476                            "superlu_" version ".tar.gz"))
 477        (sha256
 478         (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n"))))
 479     (build-system gnu-build-system)
 480     (native-inputs
 481      `(("tcsh" ,tcsh)))
 482     (inputs
 483      `(("lapack" ,lapack)
 484        ("gfortran" ,gfortran-4.8)))
 485     (arguments
 486      `(#:parallel-build? #f
 487        #:tests? #f                      ;tests are run as part of `make all`
 488        #:phases
 489        (alist-replace
 490         'configure
 491         (lambda* (#:key inputs outputs #:allow-other-keys)
 492           (call-with-output-file "make.inc"
 493             (lambda (port)
 494               (format port "
 495 PLAT        =
 496 SuperLUroot = ~a
 497 SUPERLULIB  = ~a/lib/libsuperlu.a
 498 TMGLIB      = libtmglib.a
 499 BLASDEF     = -DUSE_VENDOR_BLAS
 500 BLASLIB     = -L~a/lib -lblas
 501 LIBS        = $(SUPERLULIB) $(BLASLIB)
 502 ARCH        = ar
 503 ARCHFLAGS   = cr
 504 RANLIB      = ranlib
 505 CC          = gcc
 506 PIC         = -fPIC
 507 CFLAGS      = -O3 -DPRNTlevel=0 $(PIC)
 508 NOOPTS      = -O0 $(PIC)
 509 FORTRAN     = gfortran
 510 FFLAGS      = -O2 $(PIC)
 511 LOADER      = $(CC)
 512 CDEFS       = -DAdd_"
 513                       (getcwd)
 514                       (assoc-ref outputs "out")
 515                       (assoc-ref inputs "lapack")))))
 516         (alist-cons-before
 517          'build 'create-install-directories
 518          (lambda* (#:key outputs #:allow-other-keys)
 519            (for-each
 520             (lambda (dir)
 521               (mkdir-p (string-append (assoc-ref outputs "out")
 522                                       "/" dir)))
 523             '("lib" "include")))
 524          (alist-replace
 525           'install
 526           (lambda* (#:key outputs #:allow-other-keys)
 527             ;; Library is placed in lib during the build phase.  Copy over
 528             ;; headers to include.
 529             (let* ((out    (assoc-ref outputs "out"))
 530                    (incdir (string-append out "/include")))
 531               (for-each (lambda (file)
 532                           (let ((base (basename file)))
 533                             (format #t "installing `~a' to `~a'~%"
 534                                     base incdir)
 535                             (copy-file file
 536                                        (string-append incdir "/" base))))
 537                         (find-files "SRC" ".*\\.h$"))))
 538           %standard-phases)))))
 539     (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
 540     (synopsis "Supernodal direct solver for sparse linear systems")
 541     (description
 542      "SuperLU is a general purpose library for the direct solution of large,
 543 sparse, nonsymmetric systems of linear equations on high performance machines.
 544 The library is written in C and is callable from either C or Fortran.  The
 545 library routines perform an LU decomposition with partial pivoting and
 546 triangular system solves through forward and back substitution.  The library
 547 also provides threshold-based ILU factorization preconditioners.")
 548     (license license:bsd-3)))