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 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 "4.55")
 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         "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
 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
 184 is designed to interoperate with Gnumeric, LibreOffice and OpenOffice.  Data
 185 can be imported from spreadsheets, text files and database sources and it can
 186 be 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)))