gnu/packages/maths.scm

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