| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr> |
| 3 | ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> |
| 4 | ;;; Copyright © 2014 John Darrington <jmd@gnu.org> |
| 5 | ;;; Copyright © 2014, 2015 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 | ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org> |
| 11 | ;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il> |
| 12 | ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> |
| 13 | ;;; |
| 14 | ;;; This file is part of GNU Guix. |
| 15 | ;;; |
| 16 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 17 | ;;; under the terms of the GNU General Public License as published by |
| 18 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 19 | ;;; your option) any later version. |
| 20 | ;;; |
| 21 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 22 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 23 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 24 | ;;; GNU General Public License for more details. |
| 25 | ;;; |
| 26 | ;;; You should have received a copy of the GNU General Public License |
| 27 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 28 | |
| 29 | (define-module (gnu packages maths) |
| 30 | #:use-module (ice-9 regex) |
| 31 | #:use-module (gnu packages) |
| 32 | #:use-module ((guix licenses) #:prefix license:) |
| 33 | #:use-module (guix packages) |
| 34 | #:use-module (guix download) |
| 35 | #:use-module (guix svn-download) |
| 36 | #:use-module (guix utils) |
| 37 | #:use-module (guix build utils) |
| 38 | #:use-module (guix build-system cmake) |
| 39 | #:use-module (guix build-system gnu) |
| 40 | #:use-module (gnu packages algebra) |
| 41 | #:use-module (gnu packages bison) |
| 42 | #:use-module (gnu packages boost) |
| 43 | #:use-module (gnu packages check) |
| 44 | #:use-module (gnu packages cmake) |
| 45 | #:use-module (gnu packages compression) |
| 46 | #:use-module (gnu packages curl) |
| 47 | #:use-module (gnu packages elf) |
| 48 | #:use-module (gnu packages flex) |
| 49 | #:use-module (gnu packages fltk) |
| 50 | #:use-module (gnu packages fontutils) |
| 51 | #:use-module (gnu packages gettext) |
| 52 | #:use-module (gnu packages gcc) |
| 53 | #:use-module (gnu packages gd) |
| 54 | #:use-module (gnu packages ghostscript) |
| 55 | #:use-module (gnu packages glib) |
| 56 | #:use-module (gnu packages gtk) |
| 57 | #:use-module (gnu packages image) |
| 58 | #:use-module (gnu packages less) |
| 59 | #:use-module (gnu packages lisp) |
| 60 | #:use-module (gnu packages gnome) |
| 61 | #:use-module (gnu packages xorg) |
| 62 | #:use-module (gnu packages gl) |
| 63 | #:use-module (gnu packages m4) |
| 64 | #:use-module (gnu packages mpi) |
| 65 | #:use-module (gnu packages multiprecision) |
| 66 | #:use-module (gnu packages pcre) |
| 67 | #:use-module (gnu packages popt) |
| 68 | #:use-module (gnu packages perl) |
| 69 | #:use-module (gnu packages pkg-config) |
| 70 | #:use-module (gnu packages python) |
| 71 | #:use-module (gnu packages readline) |
| 72 | #:use-module (gnu packages tbb) |
| 73 | #:use-module (gnu packages tcsh) |
| 74 | #:use-module (gnu packages tcl) |
| 75 | #:use-module (gnu packages texinfo) |
| 76 | #:use-module (gnu packages texlive) |
| 77 | #:use-module (gnu packages wxwidgets) |
| 78 | #:use-module (gnu packages xml) |
| 79 | #:use-module (gnu packages zip) |
| 80 | #:use-module (srfi srfi-1)) |
| 81 | |
| 82 | (define-public units |
| 83 | (package |
| 84 | (name "units") |
| 85 | (version "2.12") |
| 86 | (source (origin |
| 87 | (method url-fetch) |
| 88 | (uri (string-append "mirror://gnu/units/units-" version |
| 89 | ".tar.gz")) |
| 90 | (sha256 (base32 |
| 91 | "1jxvjknz2jhq773jrwx9gc1df3gfy73yqmkjkygqxzpi318yls3q")))) |
| 92 | (build-system gnu-build-system) |
| 93 | (synopsis "Conversion between thousands of scales") |
| 94 | (description |
| 95 | "GNU Units converts numeric quantities between units of measure. It |
| 96 | can handle scale changes through adaptive usage of standard scale |
| 97 | prefixes (micro-, kilo-, etc.). It can also handle nonlinear |
| 98 | conversions such as Fahrenheit to Celsius. Its interpreter is powerful |
| 99 | enough to be used effectively as a scientific calculator.") |
| 100 | (license license:gpl3+) |
| 101 | (home-page "http://www.gnu.org/software/units/"))) |
| 102 | |
| 103 | (define-public double-conversion |
| 104 | (package |
| 105 | (name "double-conversion") |
| 106 | (version "1.1.5") |
| 107 | (source (origin |
| 108 | (method url-fetch) |
| 109 | (uri (string-append |
| 110 | "https://github.com/floitsch/double-conversion/archive/v" |
| 111 | version ".tar.gz")) |
| 112 | (file-name (string-append name "-" version ".tar.gz")) |
| 113 | (sha256 |
| 114 | (base32 |
| 115 | "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83")))) |
| 116 | (build-system cmake-build-system) |
| 117 | (arguments |
| 118 | '(#:test-target "test" |
| 119 | #:configure-flags '("-DBUILD_SHARED_LIBS=ON" |
| 120 | "-DBUILD_TESTING=ON"))) |
| 121 | (home-page "https://github.com/floitsch/double-conversion") |
| 122 | (synopsis "Conversion routines for IEEE doubles") |
| 123 | (description |
| 124 | "The double-conversion library provides binary-decimal and decimal-binary |
| 125 | routines for IEEE doubles. The library consists of efficient conversion |
| 126 | routines that have been extracted from the V8 JavaScript engine.") |
| 127 | (license license:bsd-3))) |
| 128 | |
| 129 | (define-public dionysus |
| 130 | (package |
| 131 | (name "dionysus") |
| 132 | (version "1.3.0") |
| 133 | (source (origin |
| 134 | (method url-fetch) |
| 135 | (uri (string-append "mirror://gnu/dionysus/dionysus-" version |
| 136 | ".tar.gz")) |
| 137 | (sha256 |
| 138 | (base32 |
| 139 | "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs")))) |
| 140 | (build-system gnu-build-system) |
| 141 | (inputs `(("tcl" ,tcl))) ;for 'tclsh' |
| 142 | (synopsis "Local search for universal constants and scientific values") |
| 143 | (description |
| 144 | "GNU Dionysus is a convenient system for quickly retrieving the values of |
| 145 | mathematical constants used in science and engineering. Values can be |
| 146 | searched using a simple command-line tool, choosing from three databases: |
| 147 | universal constants, atomic numbers, and constants related to |
| 148 | semiconductors.") |
| 149 | (license license:gpl3+) |
| 150 | (home-page "http://www.gnu.org/software/dionysus/"))) |
| 151 | |
| 152 | (define-public gsl |
| 153 | (package |
| 154 | (name "gsl") |
| 155 | (version "2.1") |
| 156 | (source |
| 157 | (origin |
| 158 | (method url-fetch) |
| 159 | (uri (string-append "mirror://gnu/gsl/gsl-" |
| 160 | version ".tar.gz")) |
| 161 | (sha256 |
| 162 | (base32 |
| 163 | "0rhcia9jhr3p1f1wybwyllwqfs9bggz99i3mi5lpyqcpff1hdbar")))) |
| 164 | (build-system gnu-build-system) |
| 165 | (arguments |
| 166 | `(#:parallel-tests? #f)) |
| 167 | (home-page "http://www.gnu.org/software/gsl/") |
| 168 | (synopsis "Numerical library for C and C++") |
| 169 | (description |
| 170 | "The GNU Scientific Library is a library for numerical analysis in C |
| 171 | and C++. It includes a wide range of mathematical routines, with over 1000 |
| 172 | functions in total. Subject areas covered by the library include: |
| 173 | differential equations, linear algebra, Fast Fourier Transforms and random |
| 174 | numbers.") |
| 175 | (license license:gpl3+))) |
| 176 | |
| 177 | (define-public glpk |
| 178 | (package |
| 179 | (name "glpk") |
| 180 | (version "4.59") |
| 181 | (source |
| 182 | (origin |
| 183 | (method url-fetch) |
| 184 | (uri (string-append "mirror://gnu/glpk/glpk-" |
| 185 | version ".tar.gz")) |
| 186 | (sha256 |
| 187 | (base32 |
| 188 | "1bpbp5z0378kaj5bqmc5m2j5h9c7553p0s2j6a28badqghpbx673")))) |
| 189 | (build-system gnu-build-system) |
| 190 | (inputs |
| 191 | `(("gmp" ,gmp))) |
| 192 | (arguments |
| 193 | `(#:configure-flags '("--with-gmp"))) |
| 194 | (home-page "http://www.gnu.org/software/glpk/") |
| 195 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
| 196 | (description |
| 197 | "GLPK is a C library for solving large-scale linear programming (LP), |
| 198 | mixed integer programming (MIP), and other related problems. It supports the |
| 199 | GNU MathProg modeling language, a subset of the AMPL language, and features a |
| 200 | translator for the language. In addition to the C library, a stand-alone |
| 201 | LP/MIP solver is included in the package.") |
| 202 | (license license:gpl3+))) |
| 203 | |
| 204 | (define-public pspp |
| 205 | (package |
| 206 | (name "pspp") |
| 207 | (version "0.8.5") |
| 208 | (source |
| 209 | (origin |
| 210 | (method url-fetch) |
| 211 | (uri (string-append "mirror://gnu/pspp/pspp-" |
| 212 | version ".tar.gz")) |
| 213 | (sha256 |
| 214 | (base32 |
| 215 | "0c8326yykidi94xi7jn27j8iqxc38vc07d4wf5zyk0l8lpzx5vz7")))) |
| 216 | (build-system gnu-build-system) |
| 217 | (inputs |
| 218 | `(("cairo" ,cairo) |
| 219 | ("fontconfig" ,fontconfig) |
| 220 | ("gettext" ,gnu-gettext) |
| 221 | ("gsl" ,gsl) |
| 222 | ("libxml2" ,libxml2) |
| 223 | ("pango" ,pango) |
| 224 | ("readline" ,readline) |
| 225 | ("gtk" ,gtk+-2) |
| 226 | ("gtksourceview" ,gtksourceview-2) |
| 227 | ("zlib" ,zlib))) |
| 228 | (native-inputs |
| 229 | `(("glib" ,glib "bin") ;for glib-genmarshal |
| 230 | ("perl" ,perl) |
| 231 | ("texinfo" ,texinfo) |
| 232 | ("pkg-config" ,pkg-config))) |
| 233 | (home-page "http://www.gnu.org/software/pspp/") |
| 234 | (synopsis "Statistical analysis") |
| 235 | (description |
| 236 | "GNU PSPP is a statistical analysis program. It can perform |
| 237 | descriptive statistics, T-tests, linear regression and non-parametric tests. |
| 238 | It features both a graphical interface as well as command-line input. PSPP |
| 239 | is designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data |
| 240 | can be imported from spreadsheets, text files and database sources and it can |
| 241 | be output in text, PostScript, PDF or HTML.") |
| 242 | (license license:gpl3+))) |
| 243 | |
| 244 | (define-public arpack-ng |
| 245 | (package |
| 246 | (name "arpack-ng") |
| 247 | (version "3.2.0") |
| 248 | (source |
| 249 | (origin |
| 250 | (method url-fetch) |
| 251 | (uri (string-append "https://github.com/opencollab/arpack-ng/archive/" |
| 252 | version ".tar.gz")) |
| 253 | (file-name (string-append name "-" version ".tar.gz")) |
| 254 | (sha256 |
| 255 | (base32 |
| 256 | "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff")))) |
| 257 | (build-system gnu-build-system) |
| 258 | (home-page "https://github.com/opencollab/arpack-ng") |
| 259 | (inputs |
| 260 | `(("lapack" ,lapack) |
| 261 | ("fortran" ,gfortran))) |
| 262 | (synopsis "Fortran subroutines for solving eigenvalue problems") |
| 263 | (description |
| 264 | "ARPACK-NG is a collection of Fortran77 subroutines designed to solve |
| 265 | large scale eigenvalue problems.") |
| 266 | (license (license:non-copyleft "file://COPYING" |
| 267 | "See COPYING in the distribution.")))) |
| 268 | |
| 269 | (define-public arpack-ng-openmpi |
| 270 | (package (inherit arpack-ng) |
| 271 | (name "arpack-ng-openmpi") |
| 272 | (inputs |
| 273 | `(("mpi" ,openmpi) |
| 274 | ,@(package-inputs arpack-ng))) |
| 275 | (arguments `(#:configure-flags '("--enable-mpi"))) |
| 276 | (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) |
| 277 | |
| 278 | (define-public lapack |
| 279 | (package |
| 280 | (name "lapack") |
| 281 | (version "3.5.0") |
| 282 | (source |
| 283 | (origin |
| 284 | (method url-fetch) |
| 285 | (uri (string-append "http://www.netlib.org/lapack/lapack-" |
| 286 | version ".tgz")) |
| 287 | (sha256 |
| 288 | (base32 |
| 289 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
| 290 | (build-system cmake-build-system) |
| 291 | (home-page "http://www.netlib.org/lapack/") |
| 292 | (inputs `(("fortran" ,gfortran) |
| 293 | ("python" ,python-2))) |
| 294 | (arguments |
| 295 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") |
| 296 | #:phases (alist-cons-before |
| 297 | 'check 'patch-python |
| 298 | (lambda* (#:key inputs #:allow-other-keys) |
| 299 | (let ((python (assoc-ref inputs "python"))) |
| 300 | (substitute* "lapack_testing.py" |
| 301 | (("/usr/bin/env python") python)))) |
| 302 | %standard-phases))) |
| 303 | (synopsis "Library for numerical linear algebra") |
| 304 | (description |
| 305 | "LAPACK is a Fortran 90 library for solving the most commonly occurring |
| 306 | problems in numerical linear algebra.") |
| 307 | (license (license:non-copyleft "file://LICENSE" |
| 308 | "See LICENSE in the distribution.")))) |
| 309 | |
| 310 | (define-public scalapack |
| 311 | (package |
| 312 | (name "scalapack") |
| 313 | (version "2.0.2") |
| 314 | (source |
| 315 | (origin |
| 316 | (method url-fetch) |
| 317 | (uri (string-append "http://www.netlib.org/scalapack/scalapack-" |
| 318 | version ".tgz")) |
| 319 | (sha256 |
| 320 | (base32 |
| 321 | "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c")))) |
| 322 | (build-system cmake-build-system) |
| 323 | (inputs |
| 324 | `(("mpi" ,openmpi) |
| 325 | ("fortran" ,gfortran) |
| 326 | ("lapack" ,lapack))) ;for testing only |
| 327 | (arguments |
| 328 | `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES"))) |
| 329 | (home-page "http://www.netlib.org/scalapack/") |
| 330 | (synopsis "Library for scalable numerical linear algebra") |
| 331 | (description |
| 332 | "ScaLAPACK is a Fortran 90 library of high-performance linear algebra |
| 333 | routines on parallel distributed memory machines. ScaLAPACK solves dense and |
| 334 | banded linear systems, least squares problems, eigenvalue problems, and |
| 335 | singular value problems.") |
| 336 | (license (license:bsd-style "file://LICENSE" |
| 337 | "See LICENSE in the distribution.")))) |
| 338 | |
| 339 | (define-public gnuplot |
| 340 | (package |
| 341 | (name "gnuplot") |
| 342 | (version "5.0.2") |
| 343 | (source |
| 344 | (origin |
| 345 | (method url-fetch) |
| 346 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" |
| 347 | version "/gnuplot-" version ".tar.gz")) |
| 348 | (sha256 |
| 349 | (base32 |
| 350 | "146qn414z96c7cc42a1kb9a4kpjc2q2hfdwk44kjjvgmfp9k2ass")))) |
| 351 | (build-system gnu-build-system) |
| 352 | (inputs `(("readline" ,readline) |
| 353 | ("cairo" ,cairo) |
| 354 | ("pango" ,pango) |
| 355 | ("gd" ,gd))) |
| 356 | (native-inputs `(("pkg-config" ,pkg-config) |
| 357 | ("texlive" ,texlive-minimal))) |
| 358 | (home-page "http://www.gnuplot.info") |
| 359 | (synopsis "Command-line driven graphing utility") |
| 360 | (description "Gnuplot is a portable command-line driven graphing |
| 361 | utility. It was originally created to allow scientists and students to |
| 362 | visualize mathematical functions and data interactively, but has grown to |
| 363 | support many non-interactive uses such as web scripting. It is also used as a |
| 364 | plotting engine by third-party applications like Octave.") |
| 365 | ;; X11 Style with the additional restriction that derived works may only be |
| 366 | ;; distributed as patches to the original. |
| 367 | (license (license:fsf-free |
| 368 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) |
| 369 | |
| 370 | (define-public hdf5 |
| 371 | (package |
| 372 | (name "hdf5") |
| 373 | (version "1.8.12") |
| 374 | (source |
| 375 | (origin |
| 376 | (method url-fetch) |
| 377 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" |
| 378 | version "/src/hdf5-" |
| 379 | version ".tar.bz2")) |
| 380 | (sha256 |
| 381 | (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d")))) |
| 382 | (build-system gnu-build-system) |
| 383 | (inputs |
| 384 | `(("zlib" ,zlib))) |
| 385 | (arguments |
| 386 | `(#:phases |
| 387 | (alist-cons-before |
| 388 | 'configure 'patch-configure |
| 389 | (lambda _ |
| 390 | (substitute* "configure" |
| 391 | (("/bin/mv") "mv"))) |
| 392 | %standard-phases))) |
| 393 | (home-page "http://www.hdfgroup.org") |
| 394 | (synopsis "Management suite for extremely large and complex data") |
| 395 | (description "HDF5 is a suite that makes possible the management of |
| 396 | extremely large and complex data collections.") |
| 397 | (license (license:x11-style |
| 398 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) |
| 399 | |
| 400 | |
| 401 | ;; For a fully featured Octave, users are strongly recommended also to install |
| 402 | ;; the following packages: texinfo, less, ghostscript, gnuplot. |
| 403 | (define-public octave |
| 404 | (package |
| 405 | (name "octave") |
| 406 | (version "4.0.0") |
| 407 | (source |
| 408 | (origin |
| 409 | (method url-fetch) |
| 410 | (uri (string-append "mirror://gnu/octave/octave-" |
| 411 | version ".tar.gz")) |
| 412 | (sha256 |
| 413 | (base32 |
| 414 | "101jr9yck798586jz4vkjcgk36zksmxf1pxrzvipgn2xgyay0zjc")))) |
| 415 | (build-system gnu-build-system) |
| 416 | (inputs |
| 417 | `(("lapack" ,lapack) |
| 418 | ("readline" ,readline) |
| 419 | ("glpk" ,glpk) |
| 420 | ("fftw" ,fftw) |
| 421 | ("fftwf" ,fftwf) |
| 422 | ("arpack" ,arpack-ng) |
| 423 | ("curl" ,curl) |
| 424 | ("pcre" ,pcre) |
| 425 | ("fltk" ,fltk) |
| 426 | ("fontconfig" ,fontconfig) |
| 427 | ("freetype" ,freetype) |
| 428 | ("hdf5" ,hdf5) |
| 429 | ("libxft" ,libxft) |
| 430 | ("mesa" ,mesa) |
| 431 | ("glu" ,glu) |
| 432 | ("zlib" ,zlib))) |
| 433 | (native-inputs |
| 434 | `(("gfortran" ,gfortran) |
| 435 | ("pkg-config" ,pkg-config) |
| 436 | ("perl" ,perl) |
| 437 | ;; The following inputs are not actually used in the build process. |
| 438 | ;; However, the ./configure gratuitously tests for their existence and |
| 439 | ;; assumes that programs not present at build time are also not, and |
| 440 | ;; can never be, available at run time! If these inputs are therefore |
| 441 | ;; not present, support for them will be built out. However, Octave |
| 442 | ;; will still run without them, albeit without the features they |
| 443 | ;; provide. |
| 444 | ("less" ,less) |
| 445 | ("texinfo" ,texinfo) |
| 446 | ("ghostscript" ,ghostscript) |
| 447 | ("gnuplot" ,gnuplot))) |
| 448 | (arguments |
| 449 | `(#:configure-flags (list (string-append "--with-shell=" |
| 450 | (assoc-ref %build-inputs "bash") |
| 451 | "/bin/sh")))) |
| 452 | (home-page "http://www.gnu.org/software/octave/") |
| 453 | (synopsis "High-level language for numerical computation") |
| 454 | (description "GNU Octave is a high-level interpreted language that is |
| 455 | specialized for numerical computations. It can be used for both linear and |
| 456 | non-linear applications and it provides great support for visualizing results. |
| 457 | Work may be performed both at the interactive command-line as well as via |
| 458 | script files.") |
| 459 | (license license:gpl3+))) |
| 460 | |
| 461 | (define-public gmsh |
| 462 | (package |
| 463 | (name "gmsh") |
| 464 | (version "2.11.0") |
| 465 | (source |
| 466 | (origin |
| 467 | (method url-fetch) |
| 468 | (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" |
| 469 | version "-source.tgz")) |
| 470 | (sha256 |
| 471 | (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b")) |
| 472 | (modules '((guix build utils))) |
| 473 | (snippet |
| 474 | ;; Remove non-free METIS code |
| 475 | '(delete-file-recursively "contrib/Metis")))) |
| 476 | (build-system cmake-build-system) |
| 477 | (propagated-inputs |
| 478 | `(("fltk" ,fltk) |
| 479 | ("gfortran" ,gfortran) |
| 480 | ("gmp" ,gmp) |
| 481 | ("hdf5" ,hdf5) |
| 482 | ("lapack" ,lapack) |
| 483 | ("mesa" ,mesa) |
| 484 | ("glu" ,glu) |
| 485 | ("libx11" ,libx11) |
| 486 | ("libxext" ,libxext))) |
| 487 | (arguments |
| 488 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" |
| 489 | "-DENABLE_BUILD_SHARED:BOOL=ON" |
| 490 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON") |
| 491 | #:phases (modify-phases %standard-phases |
| 492 | (replace |
| 493 | 'check |
| 494 | (lambda _ |
| 495 | (zero? (system* "make" "test" |
| 496 | ;; Disable this test. See |
| 497 | ;; https://geuz.org/trac/gmsh/ticket/271 |
| 498 | "ARGS=-E component8_in_a_box"))))))) |
| 499 | (home-page "http://www.geuz.org/gmsh/") |
| 500 | (synopsis "3D finite element grid generator") |
| 501 | (description "Gmsh is a 3D finite element grid generator with a built-in |
| 502 | CAD engine and post-processor. Its design goal is to provide a fast, light |
| 503 | and user-friendly meshing tool with parametric input and advanced |
| 504 | visualization capabilities. Gmsh is built around four modules: geometry, |
| 505 | mesh, solver and post-processing. The specification of any input to these |
| 506 | modules is done either interactively using the graphical user interface or in |
| 507 | ASCII text files using Gmsh's own scripting language.") |
| 508 | (license license:gpl2+))) |
| 509 | |
| 510 | (define-public petsc |
| 511 | (package |
| 512 | (name "petsc") |
| 513 | (version "3.6.2") |
| 514 | (source |
| 515 | (origin |
| 516 | (method url-fetch) |
| 517 | ;; The *-lite-* tarball does not contain the *large* documentation |
| 518 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" |
| 519 | "petsc-lite-" version ".tar.gz")) |
| 520 | (sha256 |
| 521 | (base32 "13h0m5f9xsdpps4lsp59iz2m7zkapwavq2zfkfvs3ab6sndla0l9")))) |
| 522 | (build-system gnu-build-system) |
| 523 | (native-inputs |
| 524 | `(("python" ,python-2) |
| 525 | ("perl" ,perl))) |
| 526 | (inputs |
| 527 | `(("gfortran" ,gfortran) |
| 528 | ("lapack" ,lapack) |
| 529 | ("superlu" ,superlu) |
| 530 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
| 531 | ;; leaving out opengl, as configuration seems to only be for mac |
| 532 | )) |
| 533 | (arguments |
| 534 | `(#:test-target "test" |
| 535 | #:parallel-build? #f ;build is parallel by default |
| 536 | #:configure-flags |
| 537 | `("--with-mpi=0" |
| 538 | "--with-openmp=1" |
| 539 | "--with-superlu=1" |
| 540 | ,(string-append "--with-superlu-include=" |
| 541 | (assoc-ref %build-inputs "superlu") "/include") |
| 542 | ,(string-append "--with-superlu-lib=" |
| 543 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) |
| 544 | #:phases |
| 545 | (alist-replace |
| 546 | 'configure |
| 547 | ;; PETSc's configure script is actually a python script, so we can't |
| 548 | ;; run it with bash. |
| 549 | (lambda* (#:key outputs (configure-flags '()) |
| 550 | #:allow-other-keys) |
| 551 | (let* ((prefix (assoc-ref outputs "out")) |
| 552 | (flags `(,(string-append "--prefix=" prefix) |
| 553 | ,@configure-flags))) |
| 554 | (format #t "build directory: ~s~%" (getcwd)) |
| 555 | (format #t "configure flags: ~s~%" flags) |
| 556 | (zero? (apply system* "./configure" flags)))) |
| 557 | (alist-cons-after |
| 558 | 'configure 'clean-local-references |
| 559 | ;; Try to keep build directory names from leaking into compiled code |
| 560 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 561 | (let ((out (assoc-ref outputs "out"))) |
| 562 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") |
| 563 | (((getcwd)) out)))) |
| 564 | (alist-cons-after |
| 565 | 'install 'clean-install |
| 566 | ;; Try to keep installed files from leaking build directory names. |
| 567 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 568 | (let ((out (assoc-ref outputs "out")) |
| 569 | (fortran (assoc-ref inputs "gfortran"))) |
| 570 | (substitute* (map (lambda (file) |
| 571 | (string-append out "/lib/petsc/conf/" file)) |
| 572 | '("petscvariables" "PETScConfig.cmake")) |
| 573 | (((getcwd)) out)) |
| 574 | ;; Make compiler references point to the store |
| 575 | (substitute* (string-append out "/lib/petsc/conf/petscvariables") |
| 576 | (("= g(cc|\\+\\+|fortran)" _ suffix) |
| 577 | (string-append "= " fortran "/bin/g" suffix))) |
| 578 | ;; PETSc installs some build logs, which aren't necessary. |
| 579 | (for-each (lambda (file) |
| 580 | (let ((f (string-append out "/lib/petsc/conf/" file))) |
| 581 | (when (file-exists? f) |
| 582 | (delete-file f)))) |
| 583 | '("configure.log" "make.log" "gmake.log" |
| 584 | "test.log" "error.log" "RDict.db" |
| 585 | ;; Once installed, should uninstall with Guix |
| 586 | "uninstall.py")))) |
| 587 | %standard-phases))))) |
| 588 | (home-page "http://www.mcs.anl.gov/petsc") |
| 589 | (synopsis "Library to solve PDEs") |
| 590 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
| 591 | data structures and routines for the scalable (parallel) solution of |
| 592 | scientific applications modeled by partial differential equations.") |
| 593 | (license (license:non-copyleft |
| 594 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
| 595 | |
| 596 | (define-public petsc-complex |
| 597 | (package (inherit petsc) |
| 598 | (name "petsc-complex") |
| 599 | (arguments |
| 600 | (substitute-keyword-arguments (package-arguments petsc) |
| 601 | ((#:configure-flags cf) |
| 602 | `(cons "--with-scalar-type=complex" ,cf)))) |
| 603 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
| 604 | |
| 605 | (define-public petsc-openmpi |
| 606 | (package (inherit petsc) |
| 607 | (name "petsc-openmpi") |
| 608 | (inputs |
| 609 | `(("openmpi" ,openmpi) |
| 610 | ,@(package-inputs petsc))) |
| 611 | (arguments |
| 612 | (substitute-keyword-arguments (package-arguments petsc) |
| 613 | ((#:configure-flags cf) |
| 614 | ``("--with-mpiexec=mpirun" |
| 615 | ,(string-append "--with-mpi-dir=" |
| 616 | (assoc-ref %build-inputs "openmpi")) |
| 617 | ,@(delete "--with-mpi=0" ,cf))))) |
| 618 | (synopsis "Library to solve PDEs (with MPI support)"))) |
| 619 | |
| 620 | (define-public petsc-complex-openmpi |
| 621 | (package (inherit petsc-complex) |
| 622 | (name "petsc-complex-openmpi") |
| 623 | (inputs |
| 624 | `(("openmpi" ,openmpi) |
| 625 | ,@(package-inputs petsc-complex))) |
| 626 | (arguments |
| 627 | (substitute-keyword-arguments (package-arguments petsc-complex) |
| 628 | ((#:configure-flags cf) |
| 629 | ``("--with-mpiexec=mpirun" |
| 630 | ,(string-append "--with-mpi-dir=" |
| 631 | (assoc-ref %build-inputs "openmpi")) |
| 632 | ,@(delete "--with-mpi=0" ,cf))))) |
| 633 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
| 634 | |
| 635 | (define-public slepc |
| 636 | (package |
| 637 | (name "slepc") |
| 638 | (version "3.6.2") |
| 639 | (source |
| 640 | (origin |
| 641 | (method url-fetch) |
| 642 | (uri (string-append "http://slepc.upv.es/download/download.php?" |
| 643 | "filename=slepc-" version ".tar.gz")) |
| 644 | (file-name (string-append name "-" version ".tar.gz")) |
| 645 | (sha256 |
| 646 | (base32 |
| 647 | "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a")))) |
| 648 | (build-system gnu-build-system) |
| 649 | (native-inputs |
| 650 | `(("python" ,python-2))) |
| 651 | (inputs |
| 652 | `(("arpack" ,arpack-ng) |
| 653 | ("gfortran" ,gfortran))) |
| 654 | (propagated-inputs |
| 655 | `(("petsc" ,petsc))) |
| 656 | (arguments |
| 657 | `(#:parallel-build? #f ;build is parallel by default |
| 658 | #:configure-flags |
| 659 | `(,(string-append "--with-arpack-dir=" |
| 660 | (assoc-ref %build-inputs "arpack") "/lib")) |
| 661 | #:phases |
| 662 | (modify-phases %standard-phases |
| 663 | (replace |
| 664 | 'configure |
| 665 | ;; configure is a python script, so we can't run it with bash. |
| 666 | (lambda* (#:key inputs outputs (configure-flags '()) |
| 667 | #:allow-other-keys) |
| 668 | (let* ((prefix (assoc-ref outputs "out")) |
| 669 | (flags `(,(string-append "--prefix=" prefix) |
| 670 | ,@configure-flags))) |
| 671 | (format #t "build directory: ~s~%" (getcwd)) |
| 672 | (format #t "configure flags: ~s~%" flags) |
| 673 | (setenv "SLEPC_DIR" (getcwd)) |
| 674 | (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) |
| 675 | (zero? (apply system* "./configure" flags))))) |
| 676 | (add-after |
| 677 | 'install 'delete-doc |
| 678 | ;; TODO: SLEPc installs HTML documentation alongside headers in |
| 679 | ;; $out/include. We'd like to move them to share/doc, but delete |
| 680 | ;; them for now, as they are incomplete and installing the complete |
| 681 | ;; documentation is difficult. |
| 682 | (lambda* (#:key outputs #:allow-other-keys) |
| 683 | (let* ((out (assoc-ref outputs "out"))) |
| 684 | (for-each delete-file (find-files out "\\.html$"))))) |
| 685 | (add-after |
| 686 | 'install 'clean-install |
| 687 | ;; Clean up unnecessary build logs from installation. |
| 688 | (lambda* (#:key outputs #:allow-other-keys) |
| 689 | (let ((out (assoc-ref outputs "out"))) |
| 690 | (for-each (lambda (file) |
| 691 | (let ((f (string-append out "/lib/slepc/conf/" file))) |
| 692 | (when (file-exists? f) |
| 693 | (delete-file f)))) |
| 694 | '("configure.log" "make.log" "gmake.log" |
| 695 | "test.log" "error.log" "RDict.db" |
| 696 | "uninstall.py")))))))) |
| 697 | (home-page "http://slepc.upv.es") |
| 698 | (synopsis "Scalable library for eigenproblems") |
| 699 | (description "SLEPc is a software library for the solution of large sparse |
| 700 | eigenproblems on parallel computers. It can be used for the solution of |
| 701 | linear eigenvalue problems formulated in either standard or generalized form, |
| 702 | as well as other related problems such as the singular value decomposition. |
| 703 | The emphasis of the software is on methods and techniques appropriate for |
| 704 | problems in which the associated matrices are sparse, for example, those |
| 705 | arising after the discretization of partial differential equations.") |
| 706 | (license license:lgpl3))) |
| 707 | |
| 708 | (define-public slepc-complex |
| 709 | (package (inherit slepc) |
| 710 | (name "slepc-complex") |
| 711 | (propagated-inputs |
| 712 | `(("petsc" ,petsc-complex) |
| 713 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) |
| 714 | (synopsis "Scalable library for eigenproblems (with complex scalars)"))) |
| 715 | |
| 716 | (define-public slepc-openmpi |
| 717 | (package (inherit slepc) |
| 718 | (name "slepc-openmpi") |
| 719 | (inputs |
| 720 | `(("mpi" ,openmpi) |
| 721 | ("arpack" ,arpack-ng-openmpi) |
| 722 | ,@(alist-delete "arpack" (package-inputs slepc)))) |
| 723 | (propagated-inputs |
| 724 | `(("petsc" ,petsc-openmpi) |
| 725 | ,@(alist-delete "petsc" (package-propagated-inputs slepc)))) |
| 726 | (synopsis "Scalable library for eigenproblems (with MPI support)"))) |
| 727 | |
| 728 | (define-public slepc-complex-openmpi |
| 729 | (package (inherit slepc-openmpi) |
| 730 | (name "slepc-complex-openmpi") |
| 731 | (propagated-inputs |
| 732 | `(("petsc" ,petsc-complex-openmpi) |
| 733 | ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) |
| 734 | (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) |
| 735 | |
| 736 | (define-public mumps |
| 737 | (package |
| 738 | (name "mumps") |
| 739 | (version "5.0.1") |
| 740 | (source |
| 741 | (origin |
| 742 | (method url-fetch) |
| 743 | (uri (string-append "http://mumps.enseeiht.fr/MUMPS_" |
| 744 | version ".tar.gz")) |
| 745 | (sha256 |
| 746 | (base32 |
| 747 | "1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah")) |
| 748 | (patches (list (search-patch "mumps-build-parallelism.patch"))))) |
| 749 | (build-system gnu-build-system) |
| 750 | (inputs |
| 751 | `(("fortran" ,gfortran) |
| 752 | ;; These are required for linking against mumps, but we let the user |
| 753 | ;; declare the dependency. |
| 754 | ("blas" ,openblas) |
| 755 | ("metis" ,metis) |
| 756 | ("scotch" ,scotch))) |
| 757 | (arguments |
| 758 | `(#:modules ((ice-9 match) |
| 759 | (ice-9 popen) |
| 760 | (srfi srfi-1) |
| 761 | ,@%gnu-build-system-modules) |
| 762 | #:phases |
| 763 | (modify-phases %standard-phases |
| 764 | (replace |
| 765 | 'configure |
| 766 | (lambda* (#:key inputs #:allow-other-keys) |
| 767 | (call-with-output-file "Makefile.inc" |
| 768 | (lambda (port) |
| 769 | (format port " |
| 770 | PLAT = |
| 771 | LIBEXT = .a |
| 772 | OUTC = -o |
| 773 | OUTF = -o |
| 774 | RM = rm -f~:[ |
| 775 | CC = gcc |
| 776 | FC = gfortran |
| 777 | FL = gfortran |
| 778 | INCSEQ = -I$(topdir)/libseq |
| 779 | LIBSEQ = -L$(topdir)/libseq -lmpiseq |
| 780 | LIBSEQNEEDED = libseqneeded~; |
| 781 | CC = mpicc |
| 782 | FC = mpifort |
| 783 | FL = mpifort~] |
| 784 | AR = ar vr # rules require trailing space, ugh... |
| 785 | RANLIB = ranlib |
| 786 | LIBBLAS = -L~a -lopenblas~@[ |
| 787 | SCALAP = -L~a -lscalapack~] |
| 788 | LIBOTHERS = -pthread |
| 789 | CDEFS = -DAdd_ |
| 790 | PIC = -fPIC |
| 791 | OPTF = -O2 -DALLOW_NON_INIT $(PIC) |
| 792 | OPTL = -O2 $(PIC) |
| 793 | OPTC = -O2 $(PIC) |
| 794 | INCS = $(INCSEQ) |
| 795 | LIBS = $(SCALAP) $(LIBSEQ) |
| 796 | LPORDDIR = $(topdir)/PORD/lib |
| 797 | IPORD = -I$(topdir)/PORD/include |
| 798 | LPORD = -L$(LPORDDIR) -lpord |
| 799 | ORDERINGSF = -Dpord~@[ |
| 800 | METISDIR = ~a |
| 801 | IMETIS = -I$(METISDIR)/include |
| 802 | LMETIS = -L$(METISDIR)/lib -lmetis |
| 803 | ORDERINGSF += -Dmetis~]~@[~:{ |
| 804 | SCOTCHDIR = ~a |
| 805 | ISCOTCH = -I$(SCOTCHDIR)/include |
| 806 | LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr |
| 807 | ORDERINGSF += ~a~}~] |
| 808 | ORDERINGSC = $(ORDERINGSF) |
| 809 | LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) |
| 810 | IORDERINGSF = $(ISCOTCH) |
| 811 | IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" |
| 812 | (assoc-ref inputs "mpi") |
| 813 | (assoc-ref inputs "blas") |
| 814 | (assoc-ref inputs "scalapack") |
| 815 | (assoc-ref inputs "metis") |
| 816 | (match (list (assoc-ref inputs "pt-scotch") |
| 817 | (assoc-ref inputs "scotch")) |
| 818 | ((#f #f) |
| 819 | #f) |
| 820 | ((#f scotch) |
| 821 | `((,scotch "" "-Dscotch"))) |
| 822 | ((ptscotch _) |
| 823 | `((,ptscotch |
| 824 | "-lptesmumps -lptscotch -lptscotcherr " |
| 825 | "-Dptscotch"))))))))) |
| 826 | (replace |
| 827 | 'build |
| 828 | ;; By default only the d-precision library is built. Make with "all" |
| 829 | ;; target so that all precision libraries and examples are built. |
| 830 | (lambda _ |
| 831 | (zero? (system* "make" "all" |
| 832 | (format #f "-j~a" (parallel-job-count)))))) |
| 833 | (replace |
| 834 | 'check |
| 835 | ;; Run the simple test drivers, which read test input from stdin: |
| 836 | ;; from the "real" input for the single- and double-precision |
| 837 | ;; testers, and from the "cmplx" input for complex-precision |
| 838 | ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi |
| 839 | ;; package to prefix execution with "mpirun". |
| 840 | (lambda* (#:key (exec-prefix '()) #:allow-other-keys) |
| 841 | (with-directory-excursion "examples" |
| 842 | (every |
| 843 | (lambda (prec type) |
| 844 | (let ((tester (apply open-pipe* |
| 845 | `(,OPEN_WRITE |
| 846 | ,@exec-prefix |
| 847 | ,(string-append "./" prec |
| 848 | "simpletest")))) |
| 849 | (input (open-input-file |
| 850 | (string-append "input_simpletest_" type)))) |
| 851 | (begin |
| 852 | (dump-port input tester) |
| 853 | (close-port input) |
| 854 | (zero? (close-pipe tester))))) |
| 855 | '("s" "d" "c" "z") |
| 856 | '("real" "real" "cmplx" "cmplx"))))) |
| 857 | (replace |
| 858 | 'install |
| 859 | (lambda* (#:key outputs #:allow-other-keys) |
| 860 | (let ((out (assoc-ref outputs "out"))) |
| 861 | (copy-recursively "lib" (string-append out "/lib")) |
| 862 | (copy-recursively "include" (string-append out "/include")) |
| 863 | (when (file-exists? "libseq/libmpiseq.a") |
| 864 | (copy-file "libseq/libmpiseq.a" |
| 865 | (string-append out "/lib/libmpiseq.a"))))))))) |
| 866 | (home-page "http://mumps.enseeiht.fr") |
| 867 | (synopsis "Multifrontal sparse direct solver") |
| 868 | (description |
| 869 | "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a |
| 870 | sparse system of linear equations A x = b using Guassian elimination.") |
| 871 | (license license:cecill-c))) |
| 872 | |
| 873 | (define-public mumps-metis |
| 874 | (package (inherit mumps) |
| 875 | (name "mumps-metis") |
| 876 | (inputs |
| 877 | (alist-delete "scotch" (package-inputs mumps))))) |
| 878 | |
| 879 | (define-public mumps-openmpi |
| 880 | (package (inherit mumps) |
| 881 | (name "mumps-openmpi") |
| 882 | (inputs |
| 883 | `(("mpi" ,openmpi) |
| 884 | ("scalapack" ,scalapack) |
| 885 | ("pt-scotch" ,pt-scotch) |
| 886 | ,@(alist-delete "scotch" (package-inputs mumps)))) |
| 887 | (arguments |
| 888 | (substitute-keyword-arguments (package-arguments mumps) |
| 889 | ((#:phases phases) |
| 890 | `(modify-phases ,phases |
| 891 | (replace |
| 892 | 'check |
| 893 | (lambda _ |
| 894 | ((assoc-ref ,phases 'check) |
| 895 | #:exec-prefix '("mpirun" "-n" "2")))))))) |
| 896 | (synopsis "Multifrontal sparse direct solver (with MPI)"))) |
| 897 | |
| 898 | (define-public mumps-metis-openmpi |
| 899 | (package (inherit mumps-openmpi) |
| 900 | (name "mumps-metis-openmpi") |
| 901 | (inputs |
| 902 | (alist-delete "pt-scotch" (package-inputs mumps-openmpi))))) |
| 903 | |
| 904 | (define-public superlu |
| 905 | (package |
| 906 | (name "superlu") |
| 907 | (version "4.3") |
| 908 | (source |
| 909 | (origin |
| 910 | (method url-fetch) |
| 911 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" |
| 912 | "superlu_" version ".tar.gz")) |
| 913 | (sha256 |
| 914 | (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) |
| 915 | (build-system gnu-build-system) |
| 916 | (native-inputs |
| 917 | `(("tcsh" ,tcsh))) |
| 918 | (inputs |
| 919 | `(("lapack" ,lapack) |
| 920 | ("gfortran" ,gfortran))) |
| 921 | (arguments |
| 922 | `(#:parallel-build? #f |
| 923 | #:tests? #f ;tests are run as part of `make all` |
| 924 | #:phases |
| 925 | (alist-replace |
| 926 | 'configure |
| 927 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 928 | (call-with-output-file "make.inc" |
| 929 | (lambda (port) |
| 930 | (format port " |
| 931 | PLAT = |
| 932 | SuperLUroot = ~a |
| 933 | SUPERLULIB = ~a/lib/libsuperlu.a |
| 934 | TMGLIB = libtmglib.a |
| 935 | BLASDEF = -DUSE_VENDOR_BLAS |
| 936 | BLASLIB = -L~a/lib -lblas |
| 937 | LIBS = $(SUPERLULIB) $(BLASLIB) |
| 938 | ARCH = ar |
| 939 | ARCHFLAGS = cr |
| 940 | RANLIB = ranlib |
| 941 | CC = gcc |
| 942 | PIC = -fPIC |
| 943 | CFLAGS = -O3 -DPRNTlevel=0 $(PIC) |
| 944 | NOOPTS = -O0 $(PIC) |
| 945 | FORTRAN = gfortran |
| 946 | FFLAGS = -O2 $(PIC) |
| 947 | LOADER = $(CC) |
| 948 | CDEFS = -DAdd_" |
| 949 | (getcwd) |
| 950 | (assoc-ref outputs "out") |
| 951 | (assoc-ref inputs "lapack"))))) |
| 952 | (alist-cons-before |
| 953 | 'build 'create-install-directories |
| 954 | (lambda* (#:key outputs #:allow-other-keys) |
| 955 | (for-each |
| 956 | (lambda (dir) |
| 957 | (mkdir-p (string-append (assoc-ref outputs "out") |
| 958 | "/" dir))) |
| 959 | '("lib" "include"))) |
| 960 | (alist-replace |
| 961 | 'install |
| 962 | (lambda* (#:key outputs #:allow-other-keys) |
| 963 | ;; Library is placed in lib during the build phase. Copy over |
| 964 | ;; headers to include. |
| 965 | (let* ((out (assoc-ref outputs "out")) |
| 966 | (incdir (string-append out "/include"))) |
| 967 | (for-each (lambda (file) |
| 968 | (let ((base (basename file))) |
| 969 | (format #t "installing `~a' to `~a'~%" |
| 970 | base incdir) |
| 971 | (copy-file file |
| 972 | (string-append incdir "/" base)))) |
| 973 | (find-files "SRC" ".*\\.h$")))) |
| 974 | %standard-phases))))) |
| 975 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") |
| 976 | (synopsis "Supernodal direct solver for sparse linear systems") |
| 977 | (description |
| 978 | "SuperLU is a general purpose library for the direct solution of large, |
| 979 | sparse, nonsymmetric systems of linear equations on high performance machines. |
| 980 | The library is written in C and is callable from either C or Fortran. The |
| 981 | library routines perform an LU decomposition with partial pivoting and |
| 982 | triangular system solves through forward and back substitution. The library |
| 983 | also provides threshold-based ILU factorization preconditioners.") |
| 984 | (license license:bsd-3))) |
| 985 | |
| 986 | (define-public superlu-dist |
| 987 | (package |
| 988 | (name "superlu-dist") |
| 989 | (version "3.3") |
| 990 | (source |
| 991 | (origin |
| 992 | (method url-fetch) |
| 993 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" |
| 994 | "superlu_dist_" version ".tar.gz")) |
| 995 | (sha256 |
| 996 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) |
| 997 | (patches (list (search-patch "superlu-dist-scotchmetis.patch"))))) |
| 998 | (build-system gnu-build-system) |
| 999 | (native-inputs |
| 1000 | `(("tcsh" ,tcsh))) |
| 1001 | (inputs |
| 1002 | `(("gfortran" ,gfortran))) |
| 1003 | (propagated-inputs |
| 1004 | `(("openmpi" ,openmpi) ;headers include MPI heades |
| 1005 | ("lapack" ,lapack) ;required to link with output library |
| 1006 | ("pt-scotch" ,pt-scotch))) ;same |
| 1007 | (arguments |
| 1008 | `(#:parallel-build? #f ;race conditions using ar |
| 1009 | #:phases |
| 1010 | (alist-replace |
| 1011 | 'configure |
| 1012 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1013 | (call-with-output-file "make.inc" |
| 1014 | (lambda (port) |
| 1015 | (format port " |
| 1016 | PLAT = |
| 1017 | DSuperLUroot = ~a |
| 1018 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a |
| 1019 | BLASDEF = -DUSE_VENDOR_BLAS |
| 1020 | BLASLIB = -L~a/lib -lblas |
| 1021 | PARMETISLIB = -L~a/lib \ |
| 1022 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ |
| 1023 | -lscotch -lscotcherr -lscotcherrexit |
| 1024 | METISLIB = -L~:*~a/lib \ |
| 1025 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit |
| 1026 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) |
| 1027 | ARCH = ar |
| 1028 | ARCHFLAGS = cr |
| 1029 | RANLIB = ranlib |
| 1030 | CC = mpicc |
| 1031 | PIC = -fPIC |
| 1032 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) |
| 1033 | NOOPTS = -O0 -g $(PIC) |
| 1034 | FORTRAN = mpifort |
| 1035 | FFLAGS = -O2 -g $(PIC) |
| 1036 | LOADER = $(CC) |
| 1037 | CDEFS = -DAdd_" |
| 1038 | (getcwd) |
| 1039 | (assoc-ref outputs "out") |
| 1040 | (assoc-ref inputs "lapack") |
| 1041 | (assoc-ref inputs "pt-scotch"))))) |
| 1042 | (alist-cons-after |
| 1043 | 'unpack 'remove-broken-symlinks |
| 1044 | (lambda _ |
| 1045 | (for-each delete-file |
| 1046 | (find-files "MAKE_INC" "\\.#make\\..*"))) |
| 1047 | (alist-cons-before |
| 1048 | 'build 'create-install-directories |
| 1049 | (lambda* (#:key outputs #:allow-other-keys) |
| 1050 | (for-each |
| 1051 | (lambda (dir) |
| 1052 | (mkdir-p (string-append (assoc-ref outputs "out") |
| 1053 | "/" dir))) |
| 1054 | '("lib" "include"))) |
| 1055 | (alist-replace |
| 1056 | 'check |
| 1057 | (lambda _ |
| 1058 | (with-directory-excursion "EXAMPLE" |
| 1059 | (and |
| 1060 | (zero? (system* "mpirun" "-n" "2" |
| 1061 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) |
| 1062 | (zero? (system* "mpirun" "-n" "2" |
| 1063 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) |
| 1064 | (alist-replace |
| 1065 | 'install |
| 1066 | (lambda* (#:key outputs #:allow-other-keys) |
| 1067 | ;; Library is placed in lib during the build phase. Copy over |
| 1068 | ;; headers to include. |
| 1069 | (let* ((out (assoc-ref outputs "out")) |
| 1070 | (incdir (string-append out "/include"))) |
| 1071 | (for-each (lambda (file) |
| 1072 | (let ((base (basename file))) |
| 1073 | (format #t "installing `~a' to `~a'~%" |
| 1074 | base incdir) |
| 1075 | (copy-file file |
| 1076 | (string-append incdir "/" base)))) |
| 1077 | (find-files "SRC" ".*\\.h$")))) |
| 1078 | %standard-phases))))))) |
| 1079 | (home-page (package-home-page superlu)) |
| 1080 | (synopsis "Parallel supernodal direct solver") |
| 1081 | (description |
| 1082 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. |
| 1083 | It is targeted for distributed memory parallel machines. SuperLU_DIST is |
| 1084 | implemented in ANSI C, and MPI for communications.") |
| 1085 | (license license:bsd-3))) |
| 1086 | |
| 1087 | (define-public scotch |
| 1088 | (package |
| 1089 | (name "scotch") |
| 1090 | (version "6.0.4") |
| 1091 | (source |
| 1092 | (origin |
| 1093 | (method url-fetch) |
| 1094 | (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/" |
| 1095 | "scotch_" version ".tar.gz")) |
| 1096 | (sha256 |
| 1097 | (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm")) |
| 1098 | (patches (list (search-patch "scotch-test-threading.patch") |
| 1099 | (search-patch "pt-scotch-build-parallelism.patch"))))) |
| 1100 | (build-system gnu-build-system) |
| 1101 | (inputs |
| 1102 | `(("zlib" ,zlib) |
| 1103 | ("flex" ,flex) |
| 1104 | ("bison" ,bison))) |
| 1105 | (arguments |
| 1106 | `(#:phases |
| 1107 | (modify-phases %standard-phases |
| 1108 | (add-after |
| 1109 | 'unpack 'chdir-to-src |
| 1110 | (lambda _ (chdir "src"))) |
| 1111 | (replace |
| 1112 | 'configure |
| 1113 | (lambda _ |
| 1114 | (call-with-output-file "Makefile.inc" |
| 1115 | (lambda (port) |
| 1116 | (format port " |
| 1117 | EXE = |
| 1118 | LIB = .a |
| 1119 | OBJ = .o |
| 1120 | MAKE = make |
| 1121 | AR = ar |
| 1122 | ARFLAGS = -ruv |
| 1123 | CAT = cat |
| 1124 | CCS = gcc |
| 1125 | CCP = mpicc |
| 1126 | CCD = gcc |
| 1127 | CPPFLAGS =~{ -D~a~} |
| 1128 | CFLAGS = -O2 -g -fPIC $(CPPFLAGS) |
| 1129 | LDFLAGS = -lz -lm -lrt -lpthread |
| 1130 | CP = cp |
| 1131 | LEX = flex -Pscotchyy -olex.yy.c |
| 1132 | LN = ln |
| 1133 | MKDIR = mkdir |
| 1134 | MV = mv |
| 1135 | RANLIB = ranlib |
| 1136 | YACC = bison -pscotchyy -y -b y |
| 1137 | " |
| 1138 | '("COMMON_FILE_COMPRESS_GZ" |
| 1139 | "COMMON_PTHREAD" |
| 1140 | "COMMON_RANDOM_FIXED_SEED" |
| 1141 | ;; Prevents symbolc clashes with libesmumps |
| 1142 | "SCOTCH_RENAME" |
| 1143 | ;; XXX: Causes invalid frees in superlu-dist tests |
| 1144 | ;; "SCOTCH_PTHREAD" |
| 1145 | ;; "SCOTCH_PTHREAD_NUMBER=2" |
| 1146 | "restrict=__restrict")))))) |
| 1147 | (add-after |
| 1148 | 'build 'build-esmumps |
| 1149 | (lambda _ |
| 1150 | (zero? (system* "make" |
| 1151 | (format #f "-j~a" (parallel-job-count)) |
| 1152 | "esmumps")))) |
| 1153 | (replace |
| 1154 | 'install |
| 1155 | (lambda* (#:key outputs #:allow-other-keys) |
| 1156 | (let ((out (assoc-ref outputs "out"))) |
| 1157 | (mkdir out) |
| 1158 | (zero? (system* "make" |
| 1159 | (string-append "prefix=" out) |
| 1160 | "install")) |
| 1161 | ;; esmumps files are not installed with the above |
| 1162 | (for-each (lambda (f) |
| 1163 | (copy-file f (string-append out "/include/" f))) |
| 1164 | (find-files "../include" ".*esmumps.h$")) |
| 1165 | (for-each (lambda (f) |
| 1166 | (copy-file f (string-append out "/lib/" f))) |
| 1167 | (find-files "../lib" "^lib.*esmumps.*")))))))) |
| 1168 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") |
| 1169 | (synopsis "Programs and libraries for graph algorithms") |
| 1170 | (description "SCOTCH is a set of programs and libraries which implement |
| 1171 | the static mapping and sparse matrix reordering algorithms developed within |
| 1172 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and |
| 1173 | conquer approach, to scientific computing problems such as graph and mesh |
| 1174 | partitioning, static mapping, and sparse matrix ordering, in application |
| 1175 | domains ranging from structural mechanics to operating systems or |
| 1176 | bio-chemistry.") |
| 1177 | ;; See LICENSE_en.txt |
| 1178 | (license license:cecill-c))) |
| 1179 | |
| 1180 | (define-public pt-scotch |
| 1181 | (package (inherit scotch) |
| 1182 | (name "pt-scotch") |
| 1183 | (propagated-inputs |
| 1184 | `(("openmpi" ,openmpi))) ;Headers include MPI headers |
| 1185 | (arguments |
| 1186 | (substitute-keyword-arguments (package-arguments scotch) |
| 1187 | ((#:phases scotch-phases) |
| 1188 | `(modify-phases ,scotch-phases |
| 1189 | (replace |
| 1190 | 'build |
| 1191 | (lambda _ |
| 1192 | (and |
| 1193 | (zero? (system* "make" |
| 1194 | (format #f "-j~a" (parallel-job-count)) |
| 1195 | "ptscotch" "ptesmumps")) |
| 1196 | ;; Install the serial metis compatibility library |
| 1197 | (zero? (system* "make" "-C" "libscotchmetis" "install"))))) |
| 1198 | (replace |
| 1199 | 'check |
| 1200 | (lambda _ (zero? (system* "make" "ptcheck")))))))) |
| 1201 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
| 1202 | |
| 1203 | (define-public metis |
| 1204 | (package |
| 1205 | (name "metis") |
| 1206 | (version "5.1.0") |
| 1207 | (source |
| 1208 | (origin |
| 1209 | (method url-fetch) |
| 1210 | (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/" |
| 1211 | "metis-" version ".tar.gz")) |
| 1212 | (sha256 |
| 1213 | (base32 |
| 1214 | "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) |
| 1215 | (build-system cmake-build-system) |
| 1216 | (inputs |
| 1217 | `(("blas" ,openblas))) |
| 1218 | (arguments |
| 1219 | `(#:tests? #f ;no tests |
| 1220 | #:configure-flags `("-DSHARED=ON" |
| 1221 | ,(string-append "-DGKLIB_PATH=" (getcwd) |
| 1222 | "/metis-" ,version "/GKlib")))) |
| 1223 | (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview") |
| 1224 | (synopsis "Graph partitioning and fill-reducing matrix ordering library") |
| 1225 | (description |
| 1226 | "METIS is a set of serial programs for partitioning graphs, partitioning |
| 1227 | finite element meshes, and producing fill-reducing orderings for sparse |
| 1228 | matrices. The algorithms implemented in METIS are based on the multilevel |
| 1229 | recursive-bisection, multilevel k-way, and multi-constraint partitioning |
| 1230 | schemes.") |
| 1231 | (license license:asl2.0))) ;As of version 5.0.3 |
| 1232 | |
| 1233 | (define-public p4est |
| 1234 | (package |
| 1235 | (name "p4est") |
| 1236 | (version "1.1") |
| 1237 | (source |
| 1238 | (origin |
| 1239 | (method url-fetch) |
| 1240 | (uri (string-append "http://p4est.github.io/release/p4est-" |
| 1241 | version ".tar.gz")) |
| 1242 | (sha256 |
| 1243 | (base32 |
| 1244 | "0faina2h5qsx3m2izbzaj9bbakma1krbbjmq43wrp1hcbyijflqb")))) |
| 1245 | (build-system gnu-build-system) |
| 1246 | (inputs |
| 1247 | `(("fortran" ,gfortran) |
| 1248 | ("blas" ,openblas) |
| 1249 | ("lapack" ,lapack) |
| 1250 | ("zlib" ,zlib))) |
| 1251 | (arguments |
| 1252 | `(#:configure-flags `(,(string-append "BLAS_LIBS=-L" |
| 1253 | (assoc-ref %build-inputs "blas") |
| 1254 | " -lopenblas") |
| 1255 | ,(string-append "LAPACK_LIBS=-L" |
| 1256 | (assoc-ref %build-inputs "lapack") |
| 1257 | " -llapack")))) |
| 1258 | (home-page "http://www.p4est.org") |
| 1259 | (synopsis "Adaptive mesh refinement on forests of octrees") |
| 1260 | (description |
| 1261 | "The p4est software library enables the dynamic management of a |
| 1262 | collection of adaptive octrees, conveniently called a forest of octrees. |
| 1263 | p4est is designed to work in parallel and scales to hundreds of thousands of |
| 1264 | processor cores.") |
| 1265 | (license license:gpl2+))) |
| 1266 | |
| 1267 | (define-public p4est-openmpi |
| 1268 | (package (inherit p4est) |
| 1269 | (name "p4est-openmpi") |
| 1270 | (inputs |
| 1271 | `(("mpi" ,openmpi) |
| 1272 | ,@(package-inputs p4est))) |
| 1273 | (arguments |
| 1274 | (substitute-keyword-arguments (package-arguments p4est) |
| 1275 | ((#:configure-flags cf) |
| 1276 | ``("--enable-mpi" ,@,cf)))) |
| 1277 | (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) |
| 1278 | |
| 1279 | (define-public gsegrafix |
| 1280 | (package |
| 1281 | (name "gsegrafix") |
| 1282 | (version "1.0.6") |
| 1283 | (source |
| 1284 | (origin |
| 1285 | (method url-fetch) |
| 1286 | (uri (string-append "mirror://gnu/" name "/" name "-" |
| 1287 | version ".tar.gz")) |
| 1288 | (sha256 |
| 1289 | (base32 |
| 1290 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) |
| 1291 | (build-system gnu-build-system) |
| 1292 | (arguments |
| 1293 | `(#:configure-flags '("LDFLAGS=-lm"))) |
| 1294 | (inputs |
| 1295 | `(("libgnomecanvas" ,libgnomecanvas) |
| 1296 | ("libbonoboui" ,libbonoboui) |
| 1297 | ("libgnomeui" ,libgnomeui) |
| 1298 | ("libgnomeprintui" ,libgnomeprintui) |
| 1299 | ("popt" ,popt))) |
| 1300 | (native-inputs |
| 1301 | `(("pkg-config" ,pkg-config))) |
| 1302 | (home-page "http://www.gnu.org/software/gsegrafix/") |
| 1303 | (synopsis "GNOME application to create scientific and engineering plots") |
| 1304 | (description "GSEGrafix is an application which produces high-quality graphical |
| 1305 | plots for science and engineering. Plots are specified via simple ASCII |
| 1306 | parameter files and data files and are presented in an anti-aliased GNOME |
| 1307 | canvas. The program supports rectangular two-dimensional plots, histograms, |
| 1308 | polar-axis plots and three-dimensional plots. Plots can be printed or saved |
| 1309 | to BMP, JPEG or PNG image formats.") |
| 1310 | (license license:gpl3+))) |
| 1311 | |
| 1312 | (define-public maxima |
| 1313 | (package |
| 1314 | (name "maxima") |
| 1315 | (version "5.36.1") |
| 1316 | (source |
| 1317 | (origin |
| 1318 | (method url-fetch) |
| 1319 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" |
| 1320 | version "-source/" name "-" version ".tar.gz")) |
| 1321 | (sha256 |
| 1322 | (base32 |
| 1323 | "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0")) |
| 1324 | (patches (list (search-patch "maxima-defsystem-mkdir.patch"))))) |
| 1325 | (build-system gnu-build-system) |
| 1326 | (inputs |
| 1327 | `(("gcl" ,gcl) |
| 1328 | ("gnuplot" ,gnuplot) ;for plots |
| 1329 | ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' |
| 1330 | (native-inputs |
| 1331 | `(("texinfo" ,texinfo) |
| 1332 | ("perl" ,perl))) |
| 1333 | (arguments |
| 1334 | `(#:configure-flags |
| 1335 | (list "--enable-gcl" |
| 1336 | (string-append "--with-posix-shell=" |
| 1337 | (assoc-ref %build-inputs "bash") |
| 1338 | "/bin/sh") |
| 1339 | (string-append "--with-wish=" |
| 1340 | (assoc-ref %build-inputs "tk") |
| 1341 | "/bin/wish" |
| 1342 | (let ((v ,(package-version tk))) |
| 1343 | (string-take v (string-index-right v #\.))))) |
| 1344 | ;; By default Maxima attempts to write temporary files to |
| 1345 | ;; '/tmp/nix-build-maxima-*', which won't exist at run time. |
| 1346 | ;; Work around that. |
| 1347 | #:make-flags (list "TMPDIR=/tmp") |
| 1348 | #:phases (alist-cons-before |
| 1349 | 'check 'pre-check |
| 1350 | (lambda _ |
| 1351 | (chmod "src/maxima" #o555)) |
| 1352 | ;; Make sure the doc and emacs files are found in the |
| 1353 | ;; standard location. Also configure maxima to find gnuplot |
| 1354 | ;; without having it on the PATH. |
| 1355 | (alist-cons-after |
| 1356 | 'install 'post-install |
| 1357 | (lambda* (#:key outputs inputs #:allow-other-keys) |
| 1358 | (let* ((gnuplot (assoc-ref inputs "gnuplot")) |
| 1359 | (out (assoc-ref outputs "out")) |
| 1360 | (datadir (string-append out "/share/maxima/" ,version))) |
| 1361 | (with-directory-excursion out |
| 1362 | (mkdir-p "share/emacs") |
| 1363 | (mkdir-p "share/doc") |
| 1364 | (symlink |
| 1365 | (string-append datadir "/emacs/") |
| 1366 | (string-append out "/share/emacs/site-lisp")) |
| 1367 | (symlink |
| 1368 | (string-append datadir "/doc/") |
| 1369 | (string-append out "/share/doc/maxima")) |
| 1370 | (with-atomic-file-replacement |
| 1371 | (string-append datadir "/share/maxima-init.lisp") |
| 1372 | (lambda (in out) |
| 1373 | (format out "~a ~s~a~%" |
| 1374 | "(setf $gnuplot_command " |
| 1375 | (string-append gnuplot "/bin/gnuplot") ")") |
| 1376 | (dump-port in out)))))) |
| 1377 | %standard-phases)))) |
| 1378 | (home-page "http://maxima.sourceforge.net") |
| 1379 | (synopsis "Numeric and symbolic expression manipulation") |
| 1380 | (description "Maxima is a system for the manipulation of symbolic and |
| 1381 | numerical expressions. It yields high precision numeric results by using |
| 1382 | exact fractions, arbitrary precision integers, and variable precision floating |
| 1383 | point numbers.") |
| 1384 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
| 1385 | ;; Others simply say "GNU General Public License" without stating a |
| 1386 | ;; version (which implicitly means gpl1+). |
| 1387 | ;; At least one file (src/maxima.asd) says "version 2." |
| 1388 | ;; GPLv2 only is therefore the smallest subset. |
| 1389 | (license license:gpl2))) |
| 1390 | |
| 1391 | (define-public wxmaxima |
| 1392 | (package |
| 1393 | (name "wxmaxima") |
| 1394 | (version "15.04.0") |
| 1395 | (source |
| 1396 | (origin |
| 1397 | (method url-fetch) |
| 1398 | (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/" |
| 1399 | version "/" name "-" version ".tar.gz")) |
| 1400 | (sha256 |
| 1401 | (base32 |
| 1402 | "1fm47ah4aw5qdjqhkz67w5fwhy8yfffa5z896crp0d3hk2bh4180")))) |
| 1403 | (build-system gnu-build-system) |
| 1404 | (inputs |
| 1405 | `(("wxwidgets" ,wxwidgets) |
| 1406 | ("maxima" ,maxima))) |
| 1407 | (arguments |
| 1408 | `(#:phases (modify-phases %standard-phases |
| 1409 | (add-after |
| 1410 | 'install 'wrap-program |
| 1411 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 1412 | (wrap-program (string-append (assoc-ref outputs "out") |
| 1413 | "/bin/wxmaxima") |
| 1414 | `("PATH" ":" prefix |
| 1415 | (,(string-append (assoc-ref inputs "maxima") |
| 1416 | "/bin")))) |
| 1417 | #t))))) |
| 1418 | (home-page "https://andrejv.github.io/wxmaxima/") |
| 1419 | (synopsis "Graphical user interface for the Maxima computer algebra system") |
| 1420 | (description |
| 1421 | "wxMaxima is a graphical user interface for the Maxima computer algebra |
| 1422 | system. It eases the use of Maxima by making most of its commands available |
| 1423 | through a menu system and by providing input dialogs for commands that require |
| 1424 | more than one argument. It also implements its own display engine that |
| 1425 | outputs mathematical symbols directly instead of depicting them with ASCII |
| 1426 | characters. |
| 1427 | |
| 1428 | wxMaxima also features 2D and 3D inline plots, simple animations, mixing of |
| 1429 | text and mathematical calculations to create documents, exporting of input and |
| 1430 | output to TeX, and a browser for Maxima's manual including command index and |
| 1431 | full text searching.") |
| 1432 | (license license:gpl2+))) |
| 1433 | |
| 1434 | (define-public armadillo |
| 1435 | (package |
| 1436 | (name "armadillo") |
| 1437 | (version "6.400.3") |
| 1438 | (source (origin |
| 1439 | (method url-fetch) |
| 1440 | (uri (string-append "mirror://sourceforge/arma/armadillo-" |
| 1441 | version ".tar.gz")) |
| 1442 | (sha256 |
| 1443 | (base32 |
| 1444 | "0bsgrmldlx77w5x26n3axj1hg6iw6csyw0dwl1flrbdwl51f9701")))) |
| 1445 | (build-system cmake-build-system) |
| 1446 | (arguments `(#:tests? #f)) ;no test target |
| 1447 | (inputs |
| 1448 | `(("openblas" ,openblas) |
| 1449 | ("lapack" ,lapack) |
| 1450 | ("arpack" ,arpack-ng))) |
| 1451 | (home-page "http://arma.sourceforge.net/") |
| 1452 | (synopsis "C++ linear algebra library") |
| 1453 | (description |
| 1454 | "Armadillo is a C++ linear algebra library, aiming towards a good balance |
| 1455 | between speed and ease of use. It is useful for algorithm development |
| 1456 | directly in C++, or quick conversion of research code into production |
| 1457 | environments. It can be used for machine learning, pattern recognition, |
| 1458 | signal processing, bioinformatics, statistics, econometrics, etc. The library |
| 1459 | provides efficient classes for vectors, matrices and cubes, as well as 150+ |
| 1460 | associated functions (eg. contiguous and non-contiguous submatrix views).") |
| 1461 | (license license:mpl2.0))) |
| 1462 | |
| 1463 | (define-public armadillo-for-rcpparmadillo |
| 1464 | (package (inherit armadillo) |
| 1465 | (version "6.200.2") |
| 1466 | (source (origin |
| 1467 | (method url-fetch) |
| 1468 | (uri (string-append "mirror://sourceforge/arma/armadillo-" |
| 1469 | version ".tar.gz")) |
| 1470 | (sha256 |
| 1471 | (base32 |
| 1472 | "1f69rlqhnf2wv8khyn2a8vi6gx1i72qgfy8b9b760ssk85dcl763")))))) |
| 1473 | |
| 1474 | (define-public muparser |
| 1475 | (package |
| 1476 | (name "muparser") |
| 1477 | (version "2.2.5") |
| 1478 | (source |
| 1479 | (origin |
| 1480 | (method svn-fetch) |
| 1481 | (uri (svn-reference |
| 1482 | (url "http://muparser.googlecode.com/svn/trunk/") |
| 1483 | (revision 34))) |
| 1484 | (sha256 |
| 1485 | (base32 |
| 1486 | "1d6bdbhx9zj3srwj3m7c9hvr18gnx1fx43h6d25my7q85gicpcwn")))) |
| 1487 | (build-system gnu-build-system) |
| 1488 | (arguments |
| 1489 | `(#:configure-flags '("--enable-samples=no") |
| 1490 | #:tests? #f)) ;no "check" target |
| 1491 | (home-page "http://muparser.beltoforion.de/") |
| 1492 | (synopsis "Fast parser library for mathematical expressions") |
| 1493 | (description |
| 1494 | "muParser is an extensible high performance math parser library. It is |
| 1495 | based on transforming an expression into a bytecode and precalculating |
| 1496 | constant parts of it.") |
| 1497 | (license license:expat))) |
| 1498 | |
| 1499 | (define-public openblas |
| 1500 | (package |
| 1501 | (name "openblas") |
| 1502 | (version "0.2.15") |
| 1503 | (source |
| 1504 | (origin |
| 1505 | (method url-fetch) |
| 1506 | (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" |
| 1507 | version)) |
| 1508 | (file-name (string-append name "-" version ".tar.gz")) |
| 1509 | (sha256 |
| 1510 | (base32 |
| 1511 | "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy")))) |
| 1512 | (build-system gnu-build-system) |
| 1513 | (arguments |
| 1514 | `(#:tests? #f ;no "check" target |
| 1515 | ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
| 1516 | ;; TARGET is specified, OpenBLAS will tune itself to the build host, so |
| 1517 | ;; we need to disable substitutions. |
| 1518 | #:substitutable? |
| 1519 | ,(let ((system (or (%current-target-system) (%current-system)))) |
| 1520 | (or (string-prefix? "x86_64" system) |
| 1521 | (string-prefix? "i686" system) |
| 1522 | (string-prefix? "mips" system))) |
| 1523 | #:make-flags |
| 1524 | (list (string-append "PREFIX=" (assoc-ref %outputs "out")) |
| 1525 | "SHELL=bash" |
| 1526 | "NO_LAPACK=1" |
| 1527 | ;; Build the library for all supported CPUs. This allows |
| 1528 | ;; switching CPU targets at runtime with the environment variable |
| 1529 | ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. |
| 1530 | ;; Unfortunately, this is not supported on non-x86 architectures, |
| 1531 | ;; where it leads to failed builds. |
| 1532 | ,@(let ((system (or (%current-target-system) (%current-system)))) |
| 1533 | (cond |
| 1534 | ((or (string-prefix? "x86_64" system) |
| 1535 | (string-prefix? "i686" system)) |
| 1536 | '("DYNAMIC_ARCH=1")) |
| 1537 | ;; On MIPS we force the "SICORTEX" TARGET, as for the other |
| 1538 | ;; two available MIPS targets special extended instructions |
| 1539 | ;; for Loongson cores are used. |
| 1540 | ((string-prefix? "mips" system) |
| 1541 | '("TARGET=SICORTEX")) |
| 1542 | (else '())))) |
| 1543 | ;; no configure script |
| 1544 | #:phases (alist-delete 'configure %standard-phases))) |
| 1545 | (inputs |
| 1546 | `(("fortran" ,gfortran))) |
| 1547 | (native-inputs |
| 1548 | `(("cunit" ,cunit) |
| 1549 | ("perl" ,perl))) |
| 1550 | (home-page "http://www.openblas.net/") |
| 1551 | (synopsis "Optimized BLAS library based on GotoBLAS") |
| 1552 | (description |
| 1553 | "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") |
| 1554 | (license license:bsd-3))) |
| 1555 | |
| 1556 | (define-public openlibm |
| 1557 | (package |
| 1558 | (name "openlibm") |
| 1559 | (version "0.4.1") |
| 1560 | (source |
| 1561 | (origin |
| 1562 | (method url-fetch) |
| 1563 | (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v" |
| 1564 | version ".tar.gz")) |
| 1565 | (file-name (string-append name "-" version ".tar.gz")) |
| 1566 | (sha256 |
| 1567 | (base32 |
| 1568 | "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn")))) |
| 1569 | (build-system gnu-build-system) |
| 1570 | (arguments |
| 1571 | `(#:make-flags |
| 1572 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 1573 | #:phases |
| 1574 | ;; no configure script |
| 1575 | (alist-delete 'configure %standard-phases) |
| 1576 | #:tests? #f)) ;the tests are part of the default target |
| 1577 | (home-page "http://openlibm.org/") |
| 1578 | (synopsis "Portable C mathematical library (libm)") |
| 1579 | (description |
| 1580 | "OpenLibm is an effort to have a high quality, portable, standalone C |
| 1581 | mathematical library (libm). It can be used standalone in applications and |
| 1582 | programming language implementations. The project was born out of a need to |
| 1583 | have a good libm for the Julia programming language that worked consistently |
| 1584 | across compilers and operating systems, and in 32-bit and 64-bit |
| 1585 | environments.") |
| 1586 | ;; See LICENSE.md for details. |
| 1587 | (license (list license:expat |
| 1588 | license:isc |
| 1589 | license:bsd-2 |
| 1590 | license:public-domain |
| 1591 | license:lgpl2.1+)))) |
| 1592 | |
| 1593 | (define-public openspecfun |
| 1594 | (package |
| 1595 | (name "openspecfun") |
| 1596 | (version "0.4") |
| 1597 | (source |
| 1598 | (origin |
| 1599 | (method url-fetch) |
| 1600 | (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v" |
| 1601 | version ".tar.gz")) |
| 1602 | (file-name (string-append name "-" version ".tar.gz")) |
| 1603 | (sha256 |
| 1604 | (base32 |
| 1605 | "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z")))) |
| 1606 | (build-system gnu-build-system) |
| 1607 | (arguments |
| 1608 | '(#:tests? #f ;no "check" target |
| 1609 | #:make-flags |
| 1610 | (list (string-append "prefix=" (assoc-ref %outputs "out"))) |
| 1611 | ;; no configure script |
| 1612 | #:phases (alist-delete 'configure %standard-phases))) |
| 1613 | (inputs |
| 1614 | `(("fortran" ,gfortran))) |
| 1615 | (home-page "https://github.com/JuliaLang/openspecfun") |
| 1616 | (synopsis "Collection of special mathematical functions") |
| 1617 | (description |
| 1618 | "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a |
| 1619 | portable package for Bessel Functions of a Complex Argument and Nonnegative |
| 1620 | Order; it contains subroutines for computing Bessel functions and Airy |
| 1621 | functions. Faddeeva allows computing the various error functions of arbitrary |
| 1622 | complex arguments (Faddeeva function, error function, complementary error |
| 1623 | function, scaled complementary error function, imaginary error function, and |
| 1624 | Dawson function); given these, one can also easily compute Voigt functions, |
| 1625 | Fresnel integrals, and similar related functions as well.") |
| 1626 | ;; Faddeeva is released under the Expat license; AMOS is included as |
| 1627 | ;; public domain software. |
| 1628 | (license (list license:expat license:public-domain)))) |
| 1629 | |
| 1630 | (define-public suitesparse |
| 1631 | (package |
| 1632 | (name "suitesparse") |
| 1633 | (version "4.4.3") |
| 1634 | (source |
| 1635 | (origin |
| 1636 | (method url-fetch) |
| 1637 | (uri (string-append |
| 1638 | "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-" |
| 1639 | version ".tar.gz")) |
| 1640 | (sha256 |
| 1641 | (base32 |
| 1642 | "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5")))) |
| 1643 | (build-system gnu-build-system) |
| 1644 | (arguments |
| 1645 | '(#:parallel-build? #f ;cholmod build fails otherwise |
| 1646 | #:tests? #f ;no "check" target |
| 1647 | #:make-flags |
| 1648 | (list "CC=gcc" |
| 1649 | "BLAS=-lblas" |
| 1650 | "TBB=-ltbb" |
| 1651 | "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used |
| 1652 | (string-append "INSTALL_LIB=" |
| 1653 | (assoc-ref %outputs "out") "/lib") |
| 1654 | (string-append "INSTALL_INCLUDE=" |
| 1655 | (assoc-ref %outputs "out") "/include")) |
| 1656 | #:phases |
| 1657 | (alist-cons-before |
| 1658 | 'install 'prepare-out |
| 1659 | ;; README.txt states that the target directories must exist prior to |
| 1660 | ;; running "make install". |
| 1661 | (lambda _ |
| 1662 | (mkdir-p (string-append (assoc-ref %outputs "out") "/lib")) |
| 1663 | (mkdir-p (string-append (assoc-ref %outputs "out") "/include"))) |
| 1664 | ;; no configure script |
| 1665 | (alist-delete 'configure %standard-phases)))) |
| 1666 | (inputs |
| 1667 | `(("tbb" ,tbb) |
| 1668 | ("lapack" ,lapack))) |
| 1669 | (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html") |
| 1670 | (synopsis "Suite of sparse matrix software") |
| 1671 | (description |
| 1672 | "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK, |
| 1673 | multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR, |
| 1674 | multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit |
| 1675 | simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and |
| 1676 | CXSparse, a concise sparse Cholesky factorization package; and many other |
| 1677 | packages.") |
| 1678 | ;; LGPLv2.1+: |
| 1679 | ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL |
| 1680 | ;; GPLv2+: |
| 1681 | ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK |
| 1682 | (license (list license:gpl2+ license:lgpl2.1+)))) |
| 1683 | |
| 1684 | (define-public atlas |
| 1685 | (package |
| 1686 | (name "atlas") |
| 1687 | (version "3.10.2") |
| 1688 | (source (origin |
| 1689 | (method url-fetch) |
| 1690 | (uri (string-append "mirror://sourceforge/math-atlas/atlas" |
| 1691 | version ".tar.bz2")) |
| 1692 | (sha256 |
| 1693 | (base32 |
| 1694 | "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars")))) |
| 1695 | (build-system gnu-build-system) |
| 1696 | (home-page "http://math-atlas.sourceforge.net/") |
| 1697 | (inputs `(("gfortran" ,gfortran) |
| 1698 | ("lapack-tar" ,(package-source lapack)))) |
| 1699 | (outputs '("out" "doc")) |
| 1700 | ;; For the moment we drop support for MIPS at it fails to compile. See |
| 1701 | ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html |
| 1702 | (supported-systems (delete "mips64el-linux" %supported-systems)) |
| 1703 | (arguments |
| 1704 | `(#:parallel-build? #f |
| 1705 | #:parallel-tests? #f |
| 1706 | |
| 1707 | ;; ATLAS tunes itself for the machine it is built on, as explained at |
| 1708 | ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>. |
| 1709 | ;; For this reason, we want users to build it locally instead of using |
| 1710 | ;; substitutes. |
| 1711 | #:substitutable? #f |
| 1712 | |
| 1713 | #:modules ((srfi srfi-26) |
| 1714 | (srfi srfi-1) |
| 1715 | (guix build gnu-build-system) |
| 1716 | (guix build utils)) |
| 1717 | #:configure-flags |
| 1718 | `(;; Generate position independent code suitable for dynamic libraries |
| 1719 | ;; and use WALL timer to get more accurate timing. |
| 1720 | "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL" |
| 1721 | ;; Set word width. |
| 1722 | "-b" |
| 1723 | ,,(if (string-match "64" (%current-system)) |
| 1724 | "64" |
| 1725 | "32") |
| 1726 | ;; Disable parallel build as it gives errors: atlas_pthread.h is |
| 1727 | ;; needed to compile C files before it is generated. |
| 1728 | "-Ss" "pmake" "make -j 1" |
| 1729 | ;; Probe is failing for MIPS. We therefore define the system |
| 1730 | ;; architecture explicitly by setting (-A) MACHINETYPE = 49 |
| 1731 | ;; 'MIPSR1xK' and (-V) ISA = 1 'none'. |
| 1732 | ,,@(if (string-prefix? "mips" (%current-system)) |
| 1733 | (list "-A" "49" "-V" "1") |
| 1734 | (list)) |
| 1735 | ;; Generate shared libraries. |
| 1736 | "--shared" |
| 1737 | ;; Build a full LAPACK library. |
| 1738 | ,(string-append "--with-netlib-lapack-tarfile=" |
| 1739 | (assoc-ref %build-inputs "lapack-tar"))) |
| 1740 | #:phases |
| 1741 | (alist-cons-after |
| 1742 | 'install 'install-doc |
| 1743 | (lambda* (#:key outputs inputs #:allow-other-keys) |
| 1744 | (let ((doc (string-append (assoc-ref outputs "doc") |
| 1745 | "/share/doc/atlas"))) |
| 1746 | (mkdir-p doc) |
| 1747 | (fold (lambda (file previous) |
| 1748 | (and previous (zero? (system* "cp" file doc)))) |
| 1749 | #t (find-files "../ATLAS/doc" ".*")))) |
| 1750 | (alist-cons-after |
| 1751 | 'check 'check-pt |
| 1752 | (lambda _ (zero? (system* "make" "ptcheck"))) |
| 1753 | ;; Fix files required to run configure. |
| 1754 | (alist-cons-before |
| 1755 | 'configure 'fix-/bin/sh |
| 1756 | (lambda _ |
| 1757 | ;; Use `sh', not `/bin/sh'. |
| 1758 | (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c") |
| 1759 | (("/bin/sh") |
| 1760 | "sh"))) |
| 1761 | ;; Fix /bin/sh in generated make files. |
| 1762 | (alist-cons-after |
| 1763 | 'configure 'fix-/bin/sh-in-generated-files |
| 1764 | (lambda _ |
| 1765 | (substitute* (find-files "." "^[Mm]ake\\.inc.*") |
| 1766 | (("/bin/sh") |
| 1767 | "sh"))) |
| 1768 | ;; ATLAS configure program does not accepts the default flags |
| 1769 | ;; passed by the 'gnu-build-system'. |
| 1770 | (alist-replace |
| 1771 | 'configure |
| 1772 | (lambda* (#:key native-inputs inputs outputs |
| 1773 | (configure-flags '()) |
| 1774 | #:allow-other-keys #:rest args) |
| 1775 | (let* ((prefix (assoc-ref outputs "out")) |
| 1776 | (bash (or (and=> (assoc-ref |
| 1777 | (or native-inputs inputs) "bash") |
| 1778 | (cut string-append <> "/bin/bash")) |
| 1779 | "/bin/sh")) |
| 1780 | (flags `(,(string-append "--prefix=" prefix) |
| 1781 | ,@configure-flags)) |
| 1782 | (abs-srcdir (getcwd)) |
| 1783 | (srcdir (string-append "../" (basename abs-srcdir)))) |
| 1784 | (format #t "source directory: ~s (relative from build: ~s)~%" |
| 1785 | abs-srcdir srcdir) |
| 1786 | (mkdir "../build") |
| 1787 | (chdir "../build") |
| 1788 | (format #t "build directory: ~s~%" (getcwd)) |
| 1789 | (format #t "configure flags: ~s~%" flags) |
| 1790 | (zero? (apply system* bash |
| 1791 | (string-append srcdir "/configure") |
| 1792 | flags)))) |
| 1793 | %standard-phases))))))) |
| 1794 | (synopsis "Automatically Tuned Linear Algebra Software") |
| 1795 | (description |
| 1796 | "ATLAS is an automatically tuned linear algebra software library |
| 1797 | providing C and Fortran77 interfaces to a portably efficient BLAS |
| 1798 | implementation, as well as a few routines from LAPACK. |
| 1799 | |
| 1800 | Optimization occurs at build time. For this reason, the library is built on |
| 1801 | the machine where it is installed, without resorting to pre-built substitutes. |
| 1802 | |
| 1803 | Before building the library, CPU throttling should be disabled. This can be |
| 1804 | done in the BIOS, or, on GNU/Linux, with the following commands: |
| 1805 | |
| 1806 | cpufreq-selector -g performance -c 0 |
| 1807 | ... |
| 1808 | cpufreq-selector -g performance -c N-1 |
| 1809 | |
| 1810 | where N is the number of cores of your CPU. Failure to do so will result in a |
| 1811 | library with poor performance.") |
| 1812 | (license license:bsd-3))) |
| 1813 | |
| 1814 | (define-public glm |
| 1815 | (package |
| 1816 | (name "glm") |
| 1817 | (version "0.9.6.3") |
| 1818 | (source |
| 1819 | (origin |
| 1820 | (method url-fetch) |
| 1821 | (uri (string-append "mirror://sourceforge/ogl-math/glm-" |
| 1822 | version ".zip")) |
| 1823 | (sha256 |
| 1824 | (base32 |
| 1825 | "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l")))) |
| 1826 | (build-system cmake-build-system) |
| 1827 | (native-inputs |
| 1828 | `(("unzip" ,unzip))) |
| 1829 | (home-page "http://glm.g-truc.net") |
| 1830 | (synopsis "OpenGL Mathematics library") |
| 1831 | (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics |
| 1832 | library for graphics software based on the OpenGL Shading Language (GLSL) |
| 1833 | specifications.") |
| 1834 | (license license:expat))) |
| 1835 | |
| 1836 | (define-public lpsolve |
| 1837 | (package |
| 1838 | (name "lpsolve") |
| 1839 | (version "5.5.2.0") |
| 1840 | (source |
| 1841 | (origin |
| 1842 | (method url-fetch) |
| 1843 | (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version |
| 1844 | "/lp_solve_" version "_source.tar.gz")) |
| 1845 | (sha256 |
| 1846 | (base32 |
| 1847 | "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq")) |
| 1848 | (modules '((guix build utils))) |
| 1849 | (snippet |
| 1850 | '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc") |
| 1851 | (("^c=cc") "c=gcc") |
| 1852 | ;; Pretend to be on a 64 bit platform to obtain a common directory |
| 1853 | ;; name for the build results on all architectures; nothing else |
| 1854 | ;; seems to depend on it. |
| 1855 | (("^PLATFORM=.*$") "PLATFORM=ux64\n"))))) |
| 1856 | (build-system gnu-build-system) |
| 1857 | (arguments |
| 1858 | `(#:tests? #f ; no check target |
| 1859 | #:phases |
| 1860 | (modify-phases %standard-phases |
| 1861 | (delete 'configure) |
| 1862 | (replace 'build |
| 1863 | (lambda _ |
| 1864 | (with-directory-excursion "lpsolve55" |
| 1865 | (system* "bash" "ccc")) |
| 1866 | (with-directory-excursion "lp_solve" |
| 1867 | (system* "bash" "ccc")) |
| 1868 | #t)) |
| 1869 | (replace 'install |
| 1870 | (lambda* (#:key outputs #:allow-other-keys) |
| 1871 | (let* ((out (assoc-ref outputs "out")) |
| 1872 | (bin (string-append out "/bin")) |
| 1873 | (lib (string-append out "/lib")) |
| 1874 | ;; This is where LibreOffice expects to find the header |
| 1875 | ;; files, and where they are installed by Debian. |
| 1876 | (include (string-append out "/include/lpsolve"))) |
| 1877 | (mkdir-p lib) |
| 1878 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.a" |
| 1879 | (string-append lib "/liblpsolve55.a")) |
| 1880 | (copy-file "lpsolve55/bin/ux64/liblpsolve55.so" |
| 1881 | (string-append lib "/liblpsolve55.so")) |
| 1882 | (install-file "lp_solve/bin/ux64/lp_solve" bin) |
| 1883 | |
| 1884 | ;; Install a subset of the header files as on Debian |
| 1885 | ;; (plus lp_bit.h, which matches the regular expression). |
| 1886 | (for-each (lambda (name) |
| 1887 | (install-file name include)) |
| 1888 | (find-files "." "lp_[HMSa-z].*\\.h$")) |
| 1889 | (with-directory-excursion "shared" |
| 1890 | (for-each (lambda (name) |
| 1891 | (install-file name include)) |
| 1892 | (find-files "." "\\.h$"))) |
| 1893 | #t)))))) |
| 1894 | (home-page "http://lpsolve.sourceforge.net/") |
| 1895 | (synopsis "Mixed integer linear programming (MILP) solver") |
| 1896 | (description |
| 1897 | "lp_solve is a mixed integer linear programming solver based on the |
| 1898 | revised simplex and the branch-and-bound methods.") |
| 1899 | (license license:lgpl2.1+))) |
| 1900 | |
| 1901 | (define-public dealii |
| 1902 | (package |
| 1903 | (name "dealii") |
| 1904 | (version "8.2.1") |
| 1905 | (source |
| 1906 | (origin |
| 1907 | (method url-fetch) |
| 1908 | (uri (string-append "https://github.com/dealii/dealii/releases/" |
| 1909 | "download/v" version "/dealii-" version ".tar.gz")) |
| 1910 | (sha256 |
| 1911 | (base32 |
| 1912 | "185jych0gdnpkjwxni7pd0dda149492zwq2457xdjg76bzj78mnp")) |
| 1913 | (patches (list (search-patch "dealii-p4est-interface.patch"))) |
| 1914 | (modules '((guix build utils))) |
| 1915 | (snippet |
| 1916 | ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost |
| 1917 | '(delete-file-recursively "bundled")))) |
| 1918 | (build-system cmake-build-system) |
| 1919 | (inputs |
| 1920 | `(("tbb" ,tbb) |
| 1921 | ("zlib" ,zlib) |
| 1922 | ("boost" ,boost) |
| 1923 | ("p4est" ,p4est) |
| 1924 | ("blas" ,openblas) |
| 1925 | ("lapack" ,lapack) |
| 1926 | ("arpack" ,arpack-ng) |
| 1927 | ("muparser" ,muparser) |
| 1928 | ("gfortran" ,gfortran) |
| 1929 | ("suitesparse" ,suitesparse))) ;for UMFPACK |
| 1930 | (arguments |
| 1931 | `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease |
| 1932 | #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure |
| 1933 | #:phases (modify-phases %standard-phases |
| 1934 | (add-after |
| 1935 | 'install 'hint-example-prefix |
| 1936 | ;; Set Cmake hints in examples so that they can find this |
| 1937 | ;; deal.II when configuring. |
| 1938 | (lambda* (#:key outputs #:allow-other-keys) |
| 1939 | (let* ((out (assoc-ref %outputs "out")) |
| 1940 | (exmpl (string-append out "/share/doc" |
| 1941 | "/dealii/examples"))) |
| 1942 | (substitute* (find-files exmpl "CMakeLists.txt") |
| 1943 | (("([[:space:]]*HINTS.*)\n" _ line) |
| 1944 | (string-append line " $ENV{HOME}/.guix-profile " |
| 1945 | out "\n"))) |
| 1946 | #t)))))) |
| 1947 | (home-page "https://www.dealii.org") |
| 1948 | (synopsis "Finite element library") |
| 1949 | (description |
| 1950 | "Deal.II is a C++ program library targeted at the computational solution |
| 1951 | of partial differential equations using adaptive finite elements. The main |
| 1952 | aim of deal.II is to enable rapid development of modern finite element codes, |
| 1953 | using among other aspects adaptive meshes and a wide array of tools often used |
| 1954 | in finite element programs.") |
| 1955 | (license license:lgpl2.1+))) |
| 1956 | |
| 1957 | (define-public dealii-openmpi |
| 1958 | (package (inherit dealii) |
| 1959 | (name "dealii-openmpi") |
| 1960 | (inputs |
| 1961 | `(("mpi" ,openmpi) |
| 1962 | ;;Supported only with MPI: |
| 1963 | ("p4est" ,p4est-openmpi) |
| 1964 | ("petsc" ,petsc-openmpi) |
| 1965 | ("slepc" ,slepc-openmpi) |
| 1966 | ("metis" ,metis) ;for MUMPS |
| 1967 | ("scalapack" ,scalapack) ;for MUMPS |
| 1968 | ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings |
| 1969 | ("arpack" ,arpack-ng-openmpi) |
| 1970 | ,@(fold alist-delete (package-inputs dealii) |
| 1971 | '("p4est" "arpack")))) |
| 1972 | (arguments |
| 1973 | (substitute-keyword-arguments (package-arguments dealii) |
| 1974 | ((#:configure-flags cf) |
| 1975 | ``("-DMPI_C_COMPILER=mpicc" |
| 1976 | "-DMPI_CXX_COMPILER=mpicxx" |
| 1977 | "-DMPI_Fortran_COMPILER=mpifort" |
| 1978 | ,@,cf)))) |
| 1979 | (synopsis "Finite element library (with MPI support)"))) |
| 1980 | |
| 1981 | (define-public flann |
| 1982 | (package |
| 1983 | (name "flann") |
| 1984 | (version "1.8.4") |
| 1985 | (source |
| 1986 | (origin |
| 1987 | (method url-fetch) |
| 1988 | (uri |
| 1989 | (string-append |
| 1990 | "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-" |
| 1991 | version "-src.zip")) |
| 1992 | (sha256 |
| 1993 | (base32 |
| 1994 | "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz")))) |
| 1995 | (build-system cmake-build-system) |
| 1996 | (native-inputs |
| 1997 | `(("unzip" ,unzip))) |
| 1998 | (inputs |
| 1999 | `(("hdf5" ,hdf5) |
| 2000 | ("octave" ,octave) |
| 2001 | ("python" ,python-2) ; print syntax |
| 2002 | ;; ("python2-numpy" ,python2-numpy) ; only required for the tests |
| 2003 | ("zlib" ,zlib))) |
| 2004 | (arguments |
| 2005 | `(#:tests? #f)) ; The test data are downloaded from the Internet. |
| 2006 | (home-page "http://www.cs.ubc.ca/research/flann/") |
| 2007 | (synopsis "Library for approximate nearest neighbors computation") |
| 2008 | (description "FLANN is a library for performing fast approximate |
| 2009 | nearest neighbor searches in high dimensional spaces. It implements a |
| 2010 | collection of algorithms and a system for automatically choosing the best |
| 2011 | algorithm and optimum parameters depending on the dataset. |
| 2012 | |
| 2013 | FLANN is written in C++ and contains bindings for C, Octave and Python.") |
| 2014 | (license (license:non-copyleft "file://COPYING" |
| 2015 | "See COPYING in the distribution.")))) |
| 2016 | |
| 2017 | (define-public wcalc |
| 2018 | (package |
| 2019 | (name "wcalc") |
| 2020 | (version "2.5") |
| 2021 | (source |
| 2022 | (origin |
| 2023 | (method url-fetch) |
| 2024 | (uri |
| 2025 | (string-append |
| 2026 | "mirror://sourceforge/w-calc/wcalc-" version ".tar.bz2")) |
| 2027 | (sha256 |
| 2028 | (base32 |
| 2029 | "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) |
| 2030 | (build-system gnu-build-system) |
| 2031 | (inputs |
| 2032 | `(("mpfr" ,mpfr) |
| 2033 | ("readline" ,readline))) |
| 2034 | (home-page "http://w-calc.sourceforge.net/index.php") |
| 2035 | (synopsis "Flexible command-line scientific calculator") |
| 2036 | (description "Wcalc is a very capable calculator. It has standard functions |
| 2037 | (sin, asin, and sinh for example, in either radians or degrees), many |
| 2038 | pre-defined constants (pi, e, c, etc.), support for using variables, \"active\" |
| 2039 | variables, a command history, hex/octal/binary input and output, unit |
| 2040 | conversions, embedded comments, and an expandable expression entry field. It |
| 2041 | evaluates expressions using the standard order of operations.") |
| 2042 | (license license:gpl2+))) |
| 2043 | |
| 2044 | (define-public xaos |
| 2045 | (package |
| 2046 | (name "xaos") |
| 2047 | (version "3.6") |
| 2048 | (source (origin |
| 2049 | (method url-fetch) |
| 2050 | (uri (string-append "mirror://sourceforge/xaos/xaos-" |
| 2051 | version ".tar.gz")) |
| 2052 | (sha256 |
| 2053 | (base32 |
| 2054 | "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq")))) |
| 2055 | (build-system gnu-build-system) |
| 2056 | (native-inputs `(("gettext" ,gnu-gettext))) |
| 2057 | (inputs `(("libx11" ,libx11) |
| 2058 | ("zlib" ,zlib) |
| 2059 | ("libpng" ,libpng) |
| 2060 | ("gsl" ,gsl))) |
| 2061 | (arguments |
| 2062 | `(#:tests? #f ;no "check" target |
| 2063 | #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale"))) |
| 2064 | (synopsis "Real-time fractal zoomer") |
| 2065 | (description "GNU XaoS is a graphical program that generates fractal |
| 2066 | patterns and allows you to zoom in and out of them infinitely in a fluid, |
| 2067 | continuous manner. It also includes tutorials that help to explain how fractals |
| 2068 | are built. It can generate many different fractal types such as the Mandelbrot |
| 2069 | set.") |
| 2070 | (home-page "http://www.gnu.org/software/xaos/") |
| 2071 | (license license:gpl2+))) |