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