| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr> |
| 3 | ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> |
| 4 | ;;; Copyright © 2014 John Darrington <jmd@gnu.org> |
| 5 | ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org> |
| 6 | ;;; |
| 7 | ;;; This file is part of GNU Guix. |
| 8 | ;;; |
| 9 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 10 | ;;; under the terms of the GNU General Public License as published by |
| 11 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 12 | ;;; your option) any later version. |
| 13 | ;;; |
| 14 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 15 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 16 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 17 | ;;; GNU General Public License for more details. |
| 18 | ;;; |
| 19 | ;;; You should have received a copy of the GNU General Public License |
| 20 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 21 | |
| 22 | (define-module (gnu packages maths) |
| 23 | #:use-module (gnu packages) |
| 24 | #:use-module ((guix licenses) |
| 25 | #:renamer (symbol-prefix-proc 'license:)) |
| 26 | #:use-module (guix packages) |
| 27 | #:use-module (guix download) |
| 28 | #:use-module (guix utils) |
| 29 | #:use-module (guix build-system cmake) |
| 30 | #:use-module (guix build-system gnu) |
| 31 | #:use-module (gnu packages algebra) |
| 32 | #:use-module (gnu packages bison) |
| 33 | #:use-module (gnu packages cmake) |
| 34 | #:use-module (gnu packages compression) |
| 35 | #:use-module (gnu packages curl) |
| 36 | #:use-module (gnu packages elf) |
| 37 | #:use-module (gnu packages flex) |
| 38 | #:use-module (gnu packages fltk) |
| 39 | #:use-module (gnu packages fontutils) |
| 40 | #:use-module (gnu packages gettext) |
| 41 | #:use-module (gnu packages gcc) |
| 42 | #:use-module (gnu packages gd) |
| 43 | #:use-module (gnu packages ghostscript) |
| 44 | #:use-module (gnu packages glib) |
| 45 | #:use-module (gnu packages gtk) |
| 46 | #:use-module (gnu packages less) |
| 47 | #:use-module (gnu packages lisp) |
| 48 | #:use-module (gnu packages gnome) |
| 49 | #:use-module (gnu packages xorg) |
| 50 | #:use-module (gnu packages gl) |
| 51 | #:use-module (gnu packages m4) |
| 52 | #:use-module (gnu packages mpi) |
| 53 | #:use-module (gnu packages multiprecision) |
| 54 | #:use-module (gnu packages pcre) |
| 55 | #:use-module (gnu packages popt) |
| 56 | #:use-module (gnu packages perl) |
| 57 | #:use-module (gnu packages pkg-config) |
| 58 | #:use-module (gnu packages python) |
| 59 | #:use-module (gnu packages readline) |
| 60 | #:use-module (gnu packages tcsh) |
| 61 | #:use-module (gnu packages texinfo) |
| 62 | #:use-module (gnu packages texlive) |
| 63 | #:use-module (gnu packages xml)) |
| 64 | |
| 65 | (define-public units |
| 66 | (package |
| 67 | (name "units") |
| 68 | (version "2.11") |
| 69 | (source (origin |
| 70 | (method url-fetch) |
| 71 | (uri (string-append "mirror://gnu/units/units-" version |
| 72 | ".tar.gz")) |
| 73 | (sha256 (base32 |
| 74 | "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk")))) |
| 75 | (build-system gnu-build-system) |
| 76 | (synopsis "Conversion between thousands of scales") |
| 77 | (description |
| 78 | "GNU Units converts numeric quantities between units of measure. It |
| 79 | can handle scale changes through adaptive usage of standard scale prefixes |
| 80 | (micro-, kilo-, etc.). It can also handle nonlinear conversions such as |
| 81 | Fahrenheit to Celsius. Its interpreter is powerful enough to be used |
| 82 | effectively as a scientific calculator.") |
| 83 | (license license:gpl3+) |
| 84 | (home-page "http://www.gnu.org/software/units/"))) |
| 85 | |
| 86 | (define-public gsl |
| 87 | (package |
| 88 | (name "gsl") |
| 89 | (version "1.16") |
| 90 | (source |
| 91 | (origin |
| 92 | (method url-fetch) |
| 93 | (uri (string-append "mirror://gnu/gsl/gsl-" |
| 94 | version ".tar.gz")) |
| 95 | (sha256 |
| 96 | (base32 |
| 97 | "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k")))) |
| 98 | (build-system gnu-build-system) |
| 99 | (arguments |
| 100 | `(#:parallel-tests? #f |
| 101 | #:phases |
| 102 | (alist-replace |
| 103 | 'configure |
| 104 | (lambda* (#:key target system outputs #:allow-other-keys #:rest args) |
| 105 | (let ((configure (assoc-ref %standard-phases 'configure))) |
| 106 | ;; disable numerically unstable test on i686, see thread at |
| 107 | ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html |
| 108 | (if (string=? (or target system) "i686-linux") |
| 109 | (substitute* "ode-initval2/Makefile.in" |
| 110 | (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS ="))) |
| 111 | (apply configure args))) |
| 112 | %standard-phases))) |
| 113 | (home-page "http://www.gnu.org/software/gsl/") |
| 114 | (synopsis "Numerical library for C and C++") |
| 115 | (description |
| 116 | "The GNU Scientific Library is a library for numerical analysis in C |
| 117 | and C++. It includes a wide range of mathematical routines, with over 1000 |
| 118 | functions in total. Subject areas covered by the library include: |
| 119 | differential equations, linear algebra, Fast Fourier Transforms and random |
| 120 | numbers.") |
| 121 | (license license:gpl3+))) |
| 122 | |
| 123 | (define-public glpk |
| 124 | (package |
| 125 | (name "glpk") |
| 126 | (version "4.54") |
| 127 | (source |
| 128 | (origin |
| 129 | (method url-fetch) |
| 130 | (uri (string-append "mirror://gnu/glpk/glpk-" |
| 131 | version ".tar.gz")) |
| 132 | (sha256 |
| 133 | (base32 |
| 134 | "18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb")))) |
| 135 | (build-system gnu-build-system) |
| 136 | (inputs |
| 137 | `(("gmp" ,gmp))) |
| 138 | (arguments |
| 139 | `(#:configure-flags '("--with-gmp"))) |
| 140 | (home-page "http://www.gnu.org/software/glpk/") |
| 141 | (synopsis "GNU Linear Programming Kit, supporting the MathProg language") |
| 142 | (description |
| 143 | "GLPK is a C library for solving large-scale linear programming (LP), |
| 144 | mixed integer programming (MIP), and other related problems. It supports the |
| 145 | GNU MathProg modeling language, a subset of the AMPL language, and features a |
| 146 | translator for the language. In addition to the C library, a stand-alone |
| 147 | LP/MIP solver is included in the package.") |
| 148 | (license license:gpl3+))) |
| 149 | |
| 150 | (define-public pspp |
| 151 | (package |
| 152 | (name "pspp") |
| 153 | (version "0.8.3") |
| 154 | (source |
| 155 | (origin |
| 156 | (method url-fetch) |
| 157 | (uri (string-append "mirror://gnu/pspp/pspp-" |
| 158 | version ".tar.gz")) |
| 159 | (sha256 |
| 160 | (base32 |
| 161 | "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d")))) |
| 162 | (build-system gnu-build-system) |
| 163 | (inputs |
| 164 | `(("cairo" ,cairo) |
| 165 | ("fontconfig" ,fontconfig) |
| 166 | ("gettext" ,gnu-gettext) |
| 167 | ("gsl" ,gsl) |
| 168 | ("libxml2" ,libxml2) |
| 169 | ("pango" ,pango) |
| 170 | ("readline" ,readline) |
| 171 | ("gtk" ,gtk+-2) |
| 172 | ("gtksourceview" ,gtksourceview) |
| 173 | ("zlib" ,zlib))) |
| 174 | (native-inputs |
| 175 | `(("glib" ,glib "bin") ;for glib-genmarshal |
| 176 | ("perl" ,perl) |
| 177 | ("pkg-config" ,pkg-config))) |
| 178 | (home-page "http://www.gnu.org/software/pspp/") |
| 179 | (synopsis "Statistical analysis") |
| 180 | (description |
| 181 | "GNU PSPP is a statistical analysis program. It can perform |
| 182 | descriptive statistics, T-tests, linear regression and non-parametric tests. |
| 183 | It features both a graphical interface as well as command-line input. PSPP is |
| 184 | designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data can |
| 185 | be imported from spreadsheets, text files and database sources and it can be |
| 186 | output in text, PostScript, PDF or HTML.") |
| 187 | (license license:gpl3+))) |
| 188 | |
| 189 | (define-public lapack |
| 190 | (package |
| 191 | (name "lapack") |
| 192 | (version "3.5.0") |
| 193 | (source |
| 194 | (origin |
| 195 | (method url-fetch) |
| 196 | (uri (string-append "http://www.netlib.org/lapack/lapack-" |
| 197 | version ".tgz")) |
| 198 | (sha256 |
| 199 | (base32 |
| 200 | "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))) |
| 201 | (build-system cmake-build-system) |
| 202 | (home-page "http://www.netlib.org/lapack/") |
| 203 | (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath |
| 204 | (inputs `(("fortran" ,gfortran-4.8) |
| 205 | ("python" ,python-2))) |
| 206 | (arguments |
| 207 | `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") |
| 208 | #:phases (alist-cons-before |
| 209 | 'check 'patch-python |
| 210 | (lambda* (#:key inputs #:allow-other-keys) |
| 211 | (let ((python (assoc-ref inputs "python"))) |
| 212 | (substitute* "lapack_testing.py" |
| 213 | (("/usr/bin/env python") python)))) |
| 214 | %standard-phases))) |
| 215 | (synopsis "Library for numerical linear algebra") |
| 216 | (description |
| 217 | "LAPACK is a Fortran 90 library for solving the most commonly occurring |
| 218 | problems in numerical linear algebra.") |
| 219 | (license (license:bsd-style "file://LICENSE" |
| 220 | "See LICENSE in the distribution.")))) |
| 221 | |
| 222 | (define-public gnuplot |
| 223 | (package |
| 224 | (name "gnuplot") |
| 225 | (version "4.6.3") |
| 226 | (source |
| 227 | (origin |
| 228 | (method url-fetch) |
| 229 | (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" |
| 230 | version "/gnuplot-" version ".tar.gz")) |
| 231 | (sha256 |
| 232 | (base32 |
| 233 | "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz")))) |
| 234 | (build-system gnu-build-system) |
| 235 | (inputs `(("readline" ,readline) |
| 236 | ("cairo" ,cairo) |
| 237 | ("pango" ,pango) |
| 238 | ("gd" ,gd))) |
| 239 | (native-inputs `(("texlive" ,texlive) |
| 240 | ("pkg-config" ,pkg-config))) |
| 241 | (home-page "http://www.gnuplot.info") |
| 242 | (synopsis "Command-line driven graphing utility") |
| 243 | (description "Gnuplot is a portable command-line driven graphing |
| 244 | utility. It was originally created to allow scientists and students to |
| 245 | visualize mathematical functions and data interactively, but has grown to |
| 246 | support many non-interactive uses such as web scripting. It is also used as a |
| 247 | plotting engine by third-party applications like Octave.") |
| 248 | ;; X11 Style with the additional restriction that derived works may only be |
| 249 | ;; distributed as patches to the original. |
| 250 | (license (license:fsf-free |
| 251 | "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) |
| 252 | |
| 253 | (define-public hdf5 |
| 254 | (package |
| 255 | (name "hdf5") |
| 256 | (version "1.8.12") |
| 257 | (source |
| 258 | (origin |
| 259 | (method url-fetch) |
| 260 | (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-" |
| 261 | version "/src/hdf5-" |
| 262 | version ".tar.bz2")) |
| 263 | (sha256 |
| 264 | (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d")))) |
| 265 | (build-system gnu-build-system) |
| 266 | (arguments |
| 267 | `(#:phases |
| 268 | (alist-cons-before |
| 269 | 'configure 'patch-configure |
| 270 | (lambda _ |
| 271 | (substitute* "configure" |
| 272 | (("/bin/mv") "mv"))) |
| 273 | %standard-phases))) |
| 274 | (outputs '("out" "bin" "lib" "include")) |
| 275 | (home-page "http://www.hdfgroup.org") |
| 276 | (synopsis "Management suite for extremely large and complex data") |
| 277 | (description "HDF5 is a suite that makes possible the management of |
| 278 | extremely large and complex data collections.") |
| 279 | (license (license:x11-style |
| 280 | "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) |
| 281 | |
| 282 | |
| 283 | ;; For a fully featured Octave, users are strongly recommended also to install |
| 284 | ;; the following packages: texinfo, less, ghostscript, gnuplot. |
| 285 | (define-public octave |
| 286 | (package |
| 287 | (name "octave") |
| 288 | (version "3.8.0") |
| 289 | (source |
| 290 | (origin |
| 291 | (method url-fetch) |
| 292 | (uri (string-append "mirror://gnu/octave/octave-" |
| 293 | version ".tar.gz")) |
| 294 | (sha256 |
| 295 | (base32 |
| 296 | "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l")))) |
| 297 | (build-system gnu-build-system) |
| 298 | (inputs |
| 299 | `(("lapack" ,lapack) |
| 300 | ("readline" ,readline) |
| 301 | ("glpk" ,glpk) |
| 302 | ("curl" ,curl) |
| 303 | ("pcre" ,pcre) |
| 304 | ("fltk" ,fltk) |
| 305 | ("fontconfig" ,fontconfig) |
| 306 | ("freetype" ,freetype) |
| 307 | ("hdf5-lib" ,hdf5 "lib") |
| 308 | ("hdf5-include" ,hdf5 "include") |
| 309 | ("libxft" ,libxft) |
| 310 | ("mesa" ,mesa) |
| 311 | ("zlib" ,zlib))) |
| 312 | (native-inputs |
| 313 | `(("gfortran" ,gfortran-4.8) |
| 314 | ("pkg-config" ,pkg-config) |
| 315 | ("perl" ,perl) |
| 316 | ;; The following inputs are not actually used in the build process. However, the |
| 317 | ;; ./configure gratuitously tests for their existence and assumes that programs not |
| 318 | ;; present at build time are also not, and can never be, available at run time! |
| 319 | ;; If these inputs are therefore not present, support for them will be built out. |
| 320 | ;; However, Octave will still run without them, albeit without the features they |
| 321 | ;; provide. |
| 322 | ("less" ,less) |
| 323 | ("texinfo" ,texinfo) |
| 324 | ("ghostscript" ,ghostscript) |
| 325 | ("gnuplot" ,gnuplot))) |
| 326 | (arguments |
| 327 | `(#:configure-flags (list (string-append "--with-shell=" |
| 328 | (assoc-ref %build-inputs "bash") |
| 329 | "/bin/sh")))) |
| 330 | (home-page "http://www.gnu.org/software/octave/") |
| 331 | (synopsis "High-level language for numerical computation") |
| 332 | (description "GNU Octave is a high-level interpreted language that is specialized |
| 333 | for numerical computations. It can be used for both linear and non-linear |
| 334 | applications and it provides great support for visualizing results. Work may |
| 335 | be performed both at the interactive command-line as well as via script |
| 336 | files.") |
| 337 | (license license:gpl3+))) |
| 338 | |
| 339 | (define-public gmsh |
| 340 | (package |
| 341 | (name "gmsh") |
| 342 | (version "2.8.4") |
| 343 | (source |
| 344 | (origin |
| 345 | (method url-fetch) |
| 346 | (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" |
| 347 | version "-source.tgz")) |
| 348 | (sha256 |
| 349 | (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr")) |
| 350 | (modules '((guix build utils))) |
| 351 | (snippet |
| 352 | ;; Remove non-free METIS code |
| 353 | '(delete-file-recursively "contrib/Metis")))) |
| 354 | (build-system cmake-build-system) |
| 355 | (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath |
| 356 | (propagated-inputs |
| 357 | `(("fltk" ,fltk) |
| 358 | ("gfortran" ,gfortran-4.8) |
| 359 | ("gmp" ,gmp) |
| 360 | ("hdf5-lib" ,hdf5 "lib") |
| 361 | ("hdf5-include" ,hdf5 "include") |
| 362 | ("lapack" ,lapack) |
| 363 | ("mesa" ,mesa) |
| 364 | ("libx11" ,libx11) |
| 365 | ("libxext" ,libxext))) |
| 366 | (arguments |
| 367 | `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" |
| 368 | "-DENABLE_BUILD_SHARED:BOOL=ON" |
| 369 | "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) |
| 370 | (home-page "http://www.geuz.org/gmsh/") |
| 371 | (synopsis "3D finite element grid generator") |
| 372 | (description "Gmsh is a 3D finite element grid generator with a built-in |
| 373 | CAD engine and post-processor. Its design goal is to provide a fast, light |
| 374 | and user-friendly meshing tool with parametric input and advanced |
| 375 | visualization capabilities. Gmsh is built around four modules: geometry, |
| 376 | mesh, solver and post-processing. The specification of any input to these |
| 377 | modules is done either interactively using the graphical user interface or in |
| 378 | ASCII text files using Gmsh's own scripting language.") |
| 379 | (license license:gpl2+))) |
| 380 | |
| 381 | (define-public petsc |
| 382 | (package |
| 383 | (name "petsc") |
| 384 | (version "3.4.4") |
| 385 | (source |
| 386 | (origin |
| 387 | (method url-fetch) |
| 388 | ;; The *-lite-* tarball does not contain the *large* documentation |
| 389 | (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" |
| 390 | "petsc-lite-" version ".tar.gz")) |
| 391 | (sha256 |
| 392 | (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv")) |
| 393 | (patches |
| 394 | (list (search-patch "petsc-fix-threadcomm.patch"))))) |
| 395 | (build-system gnu-build-system) |
| 396 | (native-inputs |
| 397 | `(("python" ,python-2) |
| 398 | ("perl" ,perl))) |
| 399 | (inputs |
| 400 | `(("gfortran" ,gfortran-4.8) |
| 401 | ("lapack" ,lapack) |
| 402 | ("superlu" ,superlu) |
| 403 | ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi |
| 404 | ;; leaving out opengl, as configuration seems to only be for mac |
| 405 | )) |
| 406 | (arguments |
| 407 | `(#:test-target "test" |
| 408 | #:parallel-build? #f |
| 409 | #:configure-flags |
| 410 | `("--with-mpi=0" |
| 411 | "--with-openmp=1" |
| 412 | "--with-superlu=1" |
| 413 | ,(string-append "--with-superlu-include=" |
| 414 | (assoc-ref %build-inputs "superlu") "/include") |
| 415 | ,(string-append "--with-superlu-lib=" |
| 416 | (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) |
| 417 | #:phases |
| 418 | (alist-replace |
| 419 | 'configure |
| 420 | ;; PETSc's configure script is actually a python script, so we can't |
| 421 | ;; run it with bash. |
| 422 | (lambda* (#:key outputs (configure-flags '()) |
| 423 | #:allow-other-keys) |
| 424 | (let* ((prefix (assoc-ref outputs "out")) |
| 425 | (flags `(,(string-append "--prefix=" prefix) |
| 426 | ,@configure-flags))) |
| 427 | (format #t "build directory: ~s~%" (getcwd)) |
| 428 | (format #t "configure flags: ~s~%" flags) |
| 429 | (zero? (apply system* "./configure" flags)))) |
| 430 | (alist-cons-after |
| 431 | 'configure 'clean-local-references |
| 432 | ;; Try to keep build directory names from leaking into compiled code |
| 433 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 434 | (let ((out (assoc-ref outputs "out"))) |
| 435 | (substitute* (find-files "." "^petsc(conf|machineinfo).h$") |
| 436 | (((getcwd)) out)))) |
| 437 | (alist-cons-after |
| 438 | 'install 'clean-install |
| 439 | ;; Try to keep installed files from leaking build directory names. |
| 440 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 441 | (let ((out (assoc-ref outputs "out")) |
| 442 | (fortran (assoc-ref inputs "gfortran"))) |
| 443 | (substitute* (map (lambda (file) |
| 444 | (string-append out "/" file)) |
| 445 | '("conf/petscvariables" |
| 446 | "conf/PETScConfig.cmake")) |
| 447 | (((getcwd)) out)) |
| 448 | ;; Make compiler references point to the store |
| 449 | (substitute* (string-append out "/conf/petscvariables") |
| 450 | (("= g(cc|\\+\\+|fortran)" _ suffix) |
| 451 | (string-append "= " fortran "/bin/g" suffix))) |
| 452 | ;; PETSc installs some build logs, which aren't necessary. |
| 453 | (for-each (lambda (file) |
| 454 | (let ((f (string-append out "/" file))) |
| 455 | (when (file-exists? f) |
| 456 | (delete-file f)))) |
| 457 | '("conf/configure.log" |
| 458 | "conf/make.log" |
| 459 | "conf/test.log" |
| 460 | "conf/error.log" |
| 461 | "conf/RDict.db" |
| 462 | ;; Once installed, should uninstall with Guix |
| 463 | "conf/uninstall.py")))) |
| 464 | %standard-phases))))) |
| 465 | (home-page "http://www.mcs.anl.gov/petsc") |
| 466 | (synopsis "Library to solve PDEs") |
| 467 | (description "PETSc, pronounced PET-see (the S is silent), is a suite of |
| 468 | data structures and routines for the scalable (parallel) solution of |
| 469 | scientific applications modeled by partial differential equations.") |
| 470 | (license (license:bsd-style |
| 471 | "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) |
| 472 | |
| 473 | (define-public petsc-complex |
| 474 | (package (inherit petsc) |
| 475 | (name "petsc-complex") |
| 476 | (arguments |
| 477 | (substitute-keyword-arguments (package-arguments petsc) |
| 478 | ((#:configure-flags cf) |
| 479 | `(cons "--with-scalar-type=complex" ,cf)))) |
| 480 | (synopsis "Library to solve PDEs (with complex scalars)"))) |
| 481 | |
| 482 | (define-public petsc-openmpi |
| 483 | (package (inherit petsc) |
| 484 | (name "petsc-openmpi") |
| 485 | (inputs |
| 486 | `(("openmpi" ,openmpi) |
| 487 | ,@(package-inputs petsc))) |
| 488 | (arguments |
| 489 | (substitute-keyword-arguments (package-arguments petsc) |
| 490 | ((#:configure-flags cf) |
| 491 | ``("--with-mpiexec=mpirun" |
| 492 | ,(string-append "--with-mpi-dir=" |
| 493 | (assoc-ref %build-inputs "openmpi")) |
| 494 | ,@(delete "--with-mpi=0" ,cf))))) |
| 495 | (synopsis "Library to solve PDEs (with MPI support)"))) |
| 496 | |
| 497 | (define-public petsc-complex-openmpi |
| 498 | (package (inherit petsc-complex) |
| 499 | (name "petsc-complex-openmpi") |
| 500 | (inputs |
| 501 | `(("openmpi" ,openmpi) |
| 502 | ,@(package-inputs petsc-complex))) |
| 503 | (arguments |
| 504 | (substitute-keyword-arguments (package-arguments petsc-complex) |
| 505 | ((#:configure-flags cf) |
| 506 | ``("--with-mpiexec=mpirun" |
| 507 | ,(string-append "--with-mpi-dir=" |
| 508 | (assoc-ref %build-inputs "openmpi")) |
| 509 | ,@(delete "--with-mpi=0" ,cf))))) |
| 510 | (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) |
| 511 | |
| 512 | (define-public superlu |
| 513 | (package |
| 514 | (name "superlu") |
| 515 | (version "4.3") |
| 516 | (source |
| 517 | (origin |
| 518 | (method url-fetch) |
| 519 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" |
| 520 | "superlu_" version ".tar.gz")) |
| 521 | (sha256 |
| 522 | (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) |
| 523 | (build-system gnu-build-system) |
| 524 | (native-inputs |
| 525 | `(("tcsh" ,tcsh))) |
| 526 | (inputs |
| 527 | `(("lapack" ,lapack) |
| 528 | ("gfortran" ,gfortran-4.8))) |
| 529 | (arguments |
| 530 | `(#:parallel-build? #f |
| 531 | #:tests? #f ;tests are run as part of `make all` |
| 532 | #:phases |
| 533 | (alist-replace |
| 534 | 'configure |
| 535 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 536 | (call-with-output-file "make.inc" |
| 537 | (lambda (port) |
| 538 | (format port " |
| 539 | PLAT = |
| 540 | SuperLUroot = ~a |
| 541 | SUPERLULIB = ~a/lib/libsuperlu.a |
| 542 | TMGLIB = libtmglib.a |
| 543 | BLASDEF = -DUSE_VENDOR_BLAS |
| 544 | BLASLIB = -L~a/lib -lblas |
| 545 | LIBS = $(SUPERLULIB) $(BLASLIB) |
| 546 | ARCH = ar |
| 547 | ARCHFLAGS = cr |
| 548 | RANLIB = ranlib |
| 549 | CC = gcc |
| 550 | PIC = -fPIC |
| 551 | CFLAGS = -O3 -DPRNTlevel=0 $(PIC) |
| 552 | NOOPTS = -O0 $(PIC) |
| 553 | FORTRAN = gfortran |
| 554 | FFLAGS = -O2 $(PIC) |
| 555 | LOADER = $(CC) |
| 556 | CDEFS = -DAdd_" |
| 557 | (getcwd) |
| 558 | (assoc-ref outputs "out") |
| 559 | (assoc-ref inputs "lapack"))))) |
| 560 | (alist-cons-before |
| 561 | 'build 'create-install-directories |
| 562 | (lambda* (#:key outputs #:allow-other-keys) |
| 563 | (for-each |
| 564 | (lambda (dir) |
| 565 | (mkdir-p (string-append (assoc-ref outputs "out") |
| 566 | "/" dir))) |
| 567 | '("lib" "include"))) |
| 568 | (alist-replace |
| 569 | 'install |
| 570 | (lambda* (#:key outputs #:allow-other-keys) |
| 571 | ;; Library is placed in lib during the build phase. Copy over |
| 572 | ;; headers to include. |
| 573 | (let* ((out (assoc-ref outputs "out")) |
| 574 | (incdir (string-append out "/include"))) |
| 575 | (for-each (lambda (file) |
| 576 | (let ((base (basename file))) |
| 577 | (format #t "installing `~a' to `~a'~%" |
| 578 | base incdir) |
| 579 | (copy-file file |
| 580 | (string-append incdir "/" base)))) |
| 581 | (find-files "SRC" ".*\\.h$")))) |
| 582 | %standard-phases))))) |
| 583 | (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") |
| 584 | (synopsis "Supernodal direct solver for sparse linear systems") |
| 585 | (description |
| 586 | "SuperLU is a general purpose library for the direct solution of large, |
| 587 | sparse, nonsymmetric systems of linear equations on high performance machines. |
| 588 | The library is written in C and is callable from either C or Fortran. The |
| 589 | library routines perform an LU decomposition with partial pivoting and |
| 590 | triangular system solves through forward and back substitution. The library |
| 591 | also provides threshold-based ILU factorization preconditioners.") |
| 592 | (license license:bsd-3))) |
| 593 | |
| 594 | (define-public superlu-dist |
| 595 | (package |
| 596 | (name "superlu-dist") |
| 597 | (version "3.3") |
| 598 | (source |
| 599 | (origin |
| 600 | (method url-fetch) |
| 601 | (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" |
| 602 | "superlu_dist_" version ".tar.gz")) |
| 603 | (sha256 |
| 604 | (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) |
| 605 | (patches (list (search-patch "superlu-dist-scotchmetis.patch"))))) |
| 606 | (build-system gnu-build-system) |
| 607 | (native-inputs |
| 608 | `(("tcsh" ,tcsh))) |
| 609 | (inputs |
| 610 | `(("gfortran" ,gfortran-4.8))) |
| 611 | (propagated-inputs |
| 612 | `(("openmpi" ,openmpi) ;headers include MPI heades |
| 613 | ("lapack" ,lapack) ;required to link with output library |
| 614 | ("pt-scotch" ,pt-scotch))) ;same |
| 615 | (arguments |
| 616 | `(#:parallel-build? #f ;race conditions using ar |
| 617 | #:phases |
| 618 | (alist-replace |
| 619 | 'configure |
| 620 | (lambda* (#:key inputs outputs #:allow-other-keys) |
| 621 | (call-with-output-file "make.inc" |
| 622 | (lambda (port) |
| 623 | (format port " |
| 624 | PLAT = |
| 625 | DSuperLUroot = ~a |
| 626 | DSUPERLULIB = ~a/lib/libsuperlu_dist.a |
| 627 | BLASDEF = -DUSE_VENDOR_BLAS |
| 628 | BLASLIB = -L~a/lib -lblas |
| 629 | PARMETISLIB = -L~a/lib \ |
| 630 | -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ |
| 631 | -lscotch -lscotcherr -lscotcherrexit |
| 632 | METISLIB = -L~:*~a/lib \ |
| 633 | -lscotchmetis -lscotch -lscotcherr -lscotcherrexit |
| 634 | LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) |
| 635 | ARCH = ar |
| 636 | ARCHFLAGS = cr |
| 637 | RANLIB = ranlib |
| 638 | CC = mpicc |
| 639 | PIC = -fPIC |
| 640 | CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) |
| 641 | NOOPTS = -O0 -g $(PIC) |
| 642 | FORTRAN = mpifort |
| 643 | FFLAGS = -O2 -g $(PIC) |
| 644 | LOADER = $(CC) |
| 645 | CDEFS = -DAdd_" |
| 646 | (getcwd) |
| 647 | (assoc-ref outputs "out") |
| 648 | (assoc-ref inputs "lapack") |
| 649 | (assoc-ref inputs "pt-scotch"))))) |
| 650 | (alist-cons-after |
| 651 | 'unpack 'remove-broken-symlinks |
| 652 | (lambda _ |
| 653 | (for-each delete-file |
| 654 | (find-files "MAKE_INC" "\\.#make\\..*"))) |
| 655 | (alist-cons-before |
| 656 | 'build 'create-install-directories |
| 657 | (lambda* (#:key outputs #:allow-other-keys) |
| 658 | (for-each |
| 659 | (lambda (dir) |
| 660 | (mkdir-p (string-append (assoc-ref outputs "out") |
| 661 | "/" dir))) |
| 662 | '("lib" "include"))) |
| 663 | (alist-replace |
| 664 | 'check |
| 665 | (lambda _ |
| 666 | (with-directory-excursion "EXAMPLE" |
| 667 | (and |
| 668 | (zero? (system* "mpirun" "-n" "2" |
| 669 | "./pddrive" "-r" "1" "-c" "2" "g20.rua")) |
| 670 | (zero? (system* "mpirun" "-n" "2" |
| 671 | "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) |
| 672 | (alist-replace |
| 673 | 'install |
| 674 | (lambda* (#:key outputs #:allow-other-keys) |
| 675 | ;; Library is placed in lib during the build phase. Copy over |
| 676 | ;; headers to include. |
| 677 | (let* ((out (assoc-ref outputs "out")) |
| 678 | (incdir (string-append out "/include"))) |
| 679 | (for-each (lambda (file) |
| 680 | (let ((base (basename file))) |
| 681 | (format #t "installing `~a' to `~a'~%" |
| 682 | base incdir) |
| 683 | (copy-file file |
| 684 | (string-append incdir "/" base)))) |
| 685 | (find-files "SRC" ".*\\.h$")))) |
| 686 | %standard-phases))))))) |
| 687 | (home-page (package-home-page superlu)) |
| 688 | (synopsis "Parallel supernodal direct solver") |
| 689 | (description |
| 690 | "SuperLU_DIST is a parallel extension to the serial SuperLU library. |
| 691 | It is targeted for distributed memory parallel machines. SuperLU_DIST is |
| 692 | implemented in ANSI C, and MPI for communications.") |
| 693 | (license license:bsd-3))) |
| 694 | |
| 695 | (define-public scotch |
| 696 | (package |
| 697 | (name "scotch") |
| 698 | (version "6.0.0") |
| 699 | (source |
| 700 | (origin |
| 701 | (method url-fetch) |
| 702 | (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/" |
| 703 | "scotch_" version ".tar.gz")) |
| 704 | (sha256 |
| 705 | (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5")) |
| 706 | (patches (list (search-patch "scotch-test-threading.patch"))))) |
| 707 | (build-system gnu-build-system) |
| 708 | (inputs |
| 709 | `(("zlib" ,zlib) |
| 710 | ("flex" ,flex) |
| 711 | ("bison" ,bison))) |
| 712 | (arguments |
| 713 | `(#:phases |
| 714 | (alist-cons-after |
| 715 | 'unpack 'chdir-to-src |
| 716 | (lambda _ (chdir "src")) |
| 717 | (alist-replace |
| 718 | 'configure |
| 719 | (lambda _ |
| 720 | (call-with-output-file "Makefile.inc" |
| 721 | (lambda (port) |
| 722 | (format port " |
| 723 | EXE = |
| 724 | LIB = .a |
| 725 | OBJ = .o |
| 726 | MAKE = make |
| 727 | AR = ar |
| 728 | ARFLAGS = -ruv |
| 729 | CCS = gcc |
| 730 | CCP = mpicc |
| 731 | CCD = gcc |
| 732 | CPPFLAGS =~{ -D~a~} |
| 733 | CFLAGS = -O2 -g $(CPPFLAGS) |
| 734 | LDFLAGS = -lz -lm -lrt -lpthread |
| 735 | CP = cp |
| 736 | LEX = flex -Pscotchyy -olex.yy.c |
| 737 | LN = ln |
| 738 | MKDIR = mkdir |
| 739 | MV = mv |
| 740 | RANLIB = ranlib |
| 741 | YACC = bison -pscotchyy -y -b y |
| 742 | " |
| 743 | '("COMMON_FILE_COMPRESS_GZ" |
| 744 | "COMMON_PTHREAD" |
| 745 | "COMMON_RANDOM_FIXED_SEED" |
| 746 | ;; TODO: Define once our MPI supports |
| 747 | ;; MPI_THREAD_MULTIPLE |
| 748 | ;; "SCOTCH_PTHREAD" |
| 749 | ;; "SCOTCH_PTHREAD_NUMBER=2" |
| 750 | "restrict=__restrict"))))) |
| 751 | (alist-replace |
| 752 | 'install |
| 753 | (lambda* (#:key outputs #:allow-other-keys) |
| 754 | (let ((out (assoc-ref outputs "out"))) |
| 755 | (mkdir out) |
| 756 | (zero? (system* "make" |
| 757 | (string-append "prefix=" out) |
| 758 | "install")))) |
| 759 | %standard-phases))))) |
| 760 | (home-page "http://www.labri.fr/perso/pelegrin/scotch/") |
| 761 | (synopsis "Programs and libraries for graph algorithms") |
| 762 | (description "SCOTCH is a set of programs and libraries which implement |
| 763 | the static mapping and sparse matrix reordering algorithms developed within |
| 764 | the SCOTCH project. Its purpose is to apply graph theory, with a divide and |
| 765 | conquer approach, to scientific computing problems such as graph and mesh |
| 766 | partitioning, static mapping, and sparse matrix ordering, in application |
| 767 | domains ranging from structural mechanics to operating systems or |
| 768 | bio-chemistry.") |
| 769 | ;; See LICENSE_en.txt |
| 770 | (license license:cecill-c))) |
| 771 | |
| 772 | (define-public pt-scotch |
| 773 | (package (inherit scotch) |
| 774 | (name "pt-scotch") |
| 775 | (propagated-inputs |
| 776 | `(("openmpi" ,openmpi))) ;Headers include MPI headers |
| 777 | (arguments |
| 778 | (substitute-keyword-arguments (package-arguments scotch) |
| 779 | ((#:phases scotch-phases) |
| 780 | `(alist-replace |
| 781 | 'build |
| 782 | ;; TODO: Would like to add parallelism here |
| 783 | (lambda _ |
| 784 | (and |
| 785 | (zero? (system* "make" "ptscotch")) |
| 786 | ;; Install the serial metis compatibility library |
| 787 | (zero? (system* "make" "-C" "libscotchmetis" "install")))) |
| 788 | (alist-replace |
| 789 | 'check |
| 790 | (lambda _ (zero? (system* "make" "ptcheck"))) |
| 791 | (alist-replace |
| 792 | 'install |
| 793 | (lambda* (#:key outputs #:allow-other-keys) |
| 794 | (let ((out (assoc-ref outputs "out"))) |
| 795 | (mkdir out) |
| 796 | (zero? (system* "make" |
| 797 | (string-append "prefix=" out) |
| 798 | "install")))) |
| 799 | ,scotch-phases)))))) |
| 800 | (synopsis "Programs and libraries for graph algorithms (with MPI)"))) |
| 801 | |
| 802 | (define-public gsegrafix |
| 803 | (package |
| 804 | (name "gsegrafix") |
| 805 | (version "1.0.6") |
| 806 | (source |
| 807 | (origin |
| 808 | (method url-fetch) |
| 809 | (uri (string-append "mirror://gnu/" name "/" name "-" |
| 810 | version ".tar.gz")) |
| 811 | (sha256 |
| 812 | (base32 |
| 813 | "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) |
| 814 | (build-system gnu-build-system) |
| 815 | (arguments |
| 816 | `(#:configure-flags '("LDFLAGS=-lm"))) |
| 817 | (inputs |
| 818 | `(("libgnomecanvas" ,libgnomecanvas) |
| 819 | ("libbonoboui" ,libbonoboui) |
| 820 | ("libgnomeui" ,libgnomeui) |
| 821 | ("libgnomeprintui" ,libgnomeprintui) |
| 822 | ("popt" ,popt))) |
| 823 | (native-inputs |
| 824 | `(("pkg-config" ,pkg-config))) |
| 825 | (home-page "http://www.gnu.org/software/gsegrafix/") |
| 826 | (synopsis "GNOME application to create scientific and engineering plots") |
| 827 | (description "GSEGrafix is an application which produces high-quality graphical |
| 828 | plots for science and engineering. Plots are specified via simple ASCII |
| 829 | parameter files and data files and are presented in an anti-aliased GNOME |
| 830 | canvas. The program supports rectangular two-dimensional plots, histograms, |
| 831 | polar-axis plots and three-dimensional plots. Plots can be printed or saved |
| 832 | to BMP, JPEG or PNG image formats.") |
| 833 | (license license:gpl3+))) |
| 834 | |
| 835 | (define-public maxima |
| 836 | (package |
| 837 | (name "maxima") |
| 838 | (version "5.33.0") |
| 839 | (source |
| 840 | (origin |
| 841 | (method url-fetch) |
| 842 | (uri (string-append "mirror://sourceforge/maxima/Maxima-source/" |
| 843 | version "-source/" name "-" version ".tar.gz")) |
| 844 | (sha256 |
| 845 | (base32 |
| 846 | "13axm11xw0f3frx5b0qdidi7igkn1524fzz77s9rbpl2yy2nrbz2")))) |
| 847 | (build-system gnu-build-system) |
| 848 | (arguments |
| 849 | `(#:phases (alist-cons-before |
| 850 | 'check 'pre-check |
| 851 | (lambda _ |
| 852 | (chmod "src/maxima" #o555)) |
| 853 | %standard-phases))) |
| 854 | (inputs |
| 855 | `(("gcl" ,gcl))) |
| 856 | (native-inputs |
| 857 | `(("texinfo" ,texinfo) |
| 858 | ("perl" ,perl))) |
| 859 | (home-page "http://maxima.sourceforge.net") |
| 860 | (synopsis "Numeric and symbolic expression manipulation") |
| 861 | (description "Maxima is a system for the manipulation of symbolic and |
| 862 | numerical expressions. It yields high precision numeric results by using |
| 863 | exact fractions, arbitrary precision integers, and variable precision floating |
| 864 | point numbers") |
| 865 | ;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+. |
| 866 | ;; Others simply say "GNU General Public License" without stating a |
| 867 | ;; version (which implicitly means gpl1+). |
| 868 | ;; At least one file (src/maxima.asd) says "version 2." |
| 869 | ;; GPLv2 only is therefore the smallest subset. |
| 870 | (license license:gpl2))) |