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