gnu/packages/julia.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
   4 ;;;
   5 ;;; This file is part of GNU Guix.
   6 ;;;
   7 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   8 ;;; under the terms of the GNU General Public License as published by
   9 ;;; the Free Software Foundation; either version 3 of the License, or (at
  10 ;;; your option) any later version.
  11 ;;;
  12 ;;; GNU Guix is distributed in the hope that it will be useful, but
  13 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  14 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15 ;;; GNU General Public License for more details.
  16 ;;;
  17 ;;; You should have received a copy of the GNU General Public License
  18 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  19
  20 (define-module (gnu packages julia)
  21   #:use-module ((guix licenses) #:prefix license:)
  22   #:use-module (guix packages)
  23   #:use-module (guix download)
  24   #:use-module (guix utils)
  25   #:use-module (guix git-download)
  26   #:use-module (guix build-system gnu)
  27   #:use-module (gnu packages)
  28   #:use-module (gnu packages algebra)
  29   #:use-module (gnu packages base)
  30   #:use-module (gnu packages compression)
  31   #:use-module (gnu packages elf)
  32   #:use-module (gnu packages gcc)
  33   #:use-module (gnu packages llvm)
  34   #:use-module (gnu packages libevent)
  35   #:use-module (gnu packages libunwind)
  36   #:use-module (gnu packages maths)
  37   #:use-module (gnu packages multiprecision) ; mpfr
  38   #:use-module (gnu packages pcre)
  39   #:use-module (gnu packages perl)
  40   #:use-module (gnu packages pkg-config)
  41   #:use-module (gnu packages python)
  42   #:use-module (gnu packages textutils)
  43   #:use-module (gnu packages tls)
  44   #:use-module (gnu packages version-control)
  45   #:use-module (gnu packages wget)
  46   #:use-module (ice-9 match))
  47
  48 (define libuv-julia
  49   (let ((commit "8d5131b6c1595920dd30644cd1435b4f344b46c8")
  50         (revision "4"))
  51     (package (inherit libuv)
  52       (name "libuv-julia")
  53       (version (string-append "1.9.0-" revision "." (string-take commit 8)))
  54       (source (origin
  55                 (method git-fetch)
  56                 (uri (git-reference
  57                       (url "https://github.com/JuliaLang/libuv.git")
  58                       (commit commit)))
  59                 (file-name (string-append name "-" version "-checkout"))
  60                 (sha256
  61                  (base32
  62                   "1fq0vhiprdryw8iisxxwyld3xdr5za6y8458p22ff56al98h22fv"))))
  63       (build-system gnu-build-system)
  64       (arguments
  65        (substitute-keyword-arguments (package-arguments libuv)
  66          ((#:phases phases)
  67           `(modify-phases ,phases
  68              (delete 'autogen)))))
  69       (home-page "https://github.com/JuliaLang/libuv"))))
  70
  71 (define libunwind-for-julia
  72   (package
  73     (inherit libunwind)
  74     (version "1.1-julia2")
  75     (source (origin
  76               (method url-fetch)
  77               (uri (string-append "https://s3.amazonaws.com/julialang/src/"
  78                                   "libunwind-" version ".tar.gz"))
  79               (sha256
  80                (base32
  81                 "0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
  82
  83 (define-public julia
  84   (package
  85     (name "julia")
  86     (version "0.5.0")
  87     (source (origin
  88               (method url-fetch)
  89               (uri (string-append
  90                     "https://github.com/JuliaLang/julia/releases/download/v"
  91                     version "/julia-" version ".tar.gz"))
  92               (sha256
  93                (base32
  94                 "0bhickil88lalp9jdj1kmf4is70zinhx8ha9rng0g3z50r4a2qmv"))))
  95     (build-system gnu-build-system)
  96     (arguments
  97      `(#:test-target "test"
  98        #:modules ((ice-9 match)
  99                   (guix build gnu-build-system)
 100                   (guix build utils))
 101
 102        ;; Do not strip binaries to keep support for full backtraces.
 103        ;; See https://github.com/JuliaLang/julia/issues/17831
 104        #:strip-binaries? #f
 105
 106        ;; The DSOs use $ORIGIN to refer to each other, but (guix build
 107        ;; gremlin) doesn't support it yet, so skip this phase.
 108        #:validate-runpath? #f
 109
 110        #:phases
 111        (modify-phases %standard-phases
 112          (delete 'configure)
 113          (add-after 'unpack 'prepare-deps
 114            (lambda* (#:key inputs #:allow-other-keys)
 115              (mkdir "deps/srccache")
 116              (copy-file (assoc-ref inputs "dsfmt")
 117                         "deps/srccache/dsfmt-2.2.3.tar.gz")
 118              (copy-file (assoc-ref inputs "objconv")
 119                         "deps/srccache/objconv.zip")
 120              (copy-file (assoc-ref inputs "suitesparse")
 121                         "deps/srccache/SuiteSparse-4.4.5.tar.gz")
 122              (copy-file (string-append (assoc-ref inputs "virtualenv")
 123                                        "/bin/virtualenv")
 124                         "julia-env")
 125              #t))
 126          (add-after 'unpack 'fix-llvm-flag
 127            (lambda _
 128              (substitute* "src/Makefile"
 129                (("-lLLVM-\\$\\(shell \\$\\(LLVM_CONFIG_HOST\\) --version\\)")
 130                 "$(shell $(LLVM_CONFIG_HOST) --libs)"))
 131              #t))
 132          (add-before 'check 'set-home
 133            ;; Some tests require a home directory to be set.
 134            (lambda _ (setenv "HOME" "/tmp") #t))
 135          (add-after 'unpack 'hardcode-soname-map
 136           ;; ./src/runtime_ccall.cpp creates a map from library names to paths
 137           ;; using the output of "/sbin/ldconfig -p".  Since ldconfig is not
 138           ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
 139           (lambda* (#:key inputs #:allow-other-keys)
 140             (use-modules (ice-9 match))
 141             (substitute* "src/runtime_ccall.cpp"
 142               (("jl_read_sonames.*;")
 143                (string-join
 144                 (map (match-lambda
 145                        ((input libname soname)
 146                         (string-append
 147                          "sonameMap[\"" libname "\"] = "
 148                          "\"" (assoc-ref inputs input) "/lib/" soname "\";")))
 149                      '(("libc"        "libc"           "libc.so.6")
 150                        ("pcre2"       "libpcre2-8"     "libpcre2-8.so")
 151                        ("mpfr"        "libmpfr"        "libmpfr.so")
 152                        ("openblas"    "libblas"        "libopenblas.so")
 153                        ("arpack-ng"   "libarpack"      "libarpack.so")
 154                        ("lapack"      "liblapack"      "liblapack.so")
 155                        ("libgit2"     "libgit2"        "libgit2.so")
 156                        ("gmp"         "libgmp"         "libgmp.so")
 157                        ("openlibm"    "libopenlibm"    "libopenlibm.so")
 158                        ("openspecfun" "libopenspecfun" "libopenspecfun.so")
 159                        ("fftw"        "libfftw3"       "libfftw3.so")
 160                        ("fftwf"       "libfftw3f"      "libfftw3f.so"))))))
 161             (substitute* "base/fft/FFTW.jl"
 162               (("const libfftw = Base.libfftw_name")
 163                (string-append "const libfftw = \""
 164                               (assoc-ref inputs "fftw") "/lib/libfftw3.so"
 165                               "\""))
 166               (("const libfftwf = Base.libfftwf_name")
 167                (string-append "const libfftwf = \""
 168                               (assoc-ref inputs "fftwf") "/lib/libfftw3f.so"
 169                               "\"")))
 170             (substitute* "base/math.jl"
 171               (("const libm = Base.libm_name")
 172                (string-append "const libm = \""
 173                               (assoc-ref inputs "openlibm")
 174                               "/lib/libopenlibm.so"
 175                               "\""))
 176               (("const openspecfun = \"libopenspecfun\"")
 177                (string-append "const openspecfun = \""
 178                               (assoc-ref inputs "openspecfun")
 179                               "/lib/libopenspecfun.so"
 180                               "\"")))
 181             (substitute* "base/pcre.jl"
 182               (("const PCRE_LIB = \"libpcre2-8\"")
 183                (string-append "const PCRE_LIB = \""
 184                               (assoc-ref inputs "pcre2")
 185                               "/lib/libpcre2-8.so" "\"")))
 186             #t))
 187          (add-before 'build 'fix-include-and-link-paths
 188           (lambda* (#:key inputs #:allow-other-keys)
 189             ;; LIBUTF8PROC is a linker flag, not a build target.  It is
 190             ;; included in the LIBFILES_* variable which is used as a
 191             ;; collection of build targets and a list of libraries to link
 192             ;; against.
 193             (substitute* "src/flisp/Makefile"
 194               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
 195                "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
 196               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
 197                "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
 198
 199             ;; The REPL must be linked with libuv.
 200             (substitute* "ui/Makefile"
 201               (("JLDFLAGS \\+= ")
 202                (string-append "JLDFLAGS += "
 203                               (assoc-ref %build-inputs "libuv")
 204                               "/lib/libuv.so ")))
 205
 206             (substitute* "base/Makefile"
 207               (("\\$\\(build_includedir\\)/uv-errno.h")
 208                (string-append (assoc-ref inputs "libuv")
 209                               "/include/uv-errno.h")))
 210             #t))
 211          (add-before 'build 'replace-default-shell
 212           (lambda _
 213             (substitute* "base/client.jl"
 214               (("/bin/sh") (which "sh")))
 215             #t))
 216          (add-after 'unpack 'hardcode-paths
 217            (lambda _
 218              (substitute* "base/interactiveutil.jl"
 219                (("`which") (string-append "`" (which "which")))
 220                (("`wget")  (string-append "`" (which "wget"))))
 221              #t))
 222          (add-before 'check 'disable-broken-tests
 223            (lambda _
 224              (substitute* "test/choosetests.jl"
 225                ;; These tests fail, probably because some of the input
 226                ;; binaries have been stripped and thus backtraces don't look
 227                ;; as expected.
 228                (("\"backtrace\",") "")
 229                (("\"compile\",") "")
 230                (("\"replutil\",") "")
 231                (("\"cmdlineargs\",") ""))
 232              #t)))
 233        #:make-flags
 234        (list
 235         (string-append "prefix=" (assoc-ref %outputs "out"))
 236
 237         ;; Passing the MARCH flag is necessary to build binary substitutes for
 238         ;; the supported architectures.
 239         ,(match (or (%current-target-system)
 240                     (%current-system))
 241            ("x86_64-linux" "MARCH=x86-64")
 242            ("i686-linux" "MARCH=pentium4")
 243            ;; Prevent errors when querying this package on unsupported
 244            ;; platforms, e.g. when running "guix package --search="
 245            (_ "MARCH=UNSUPPORTED"))
 246
 247         "CONFIG_SHELL=bash"     ;needed to build bundled libraries
 248         "USE_SYSTEM_DSFMT=0"    ;not packaged for Guix and upstream has no
 249                                 ;build system for a shared library.
 250         "USE_SYSTEM_LAPACK=1"
 251         "USE_SYSTEM_BLAS=1"
 252         "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
 253
 254         "USE_SYSTEM_FFTW=1"
 255         "LIBFFTWNAME=libfftw3"
 256         "LIBFFTWFNAME=libfftw3f"
 257
 258         ;; TODO: Suitesparse does not install shared libraries, so we cannot
 259         ;; use the suitesparse package.
 260         ;; "USE_SYSTEM_SUITESPARSE=1"
 261         ;; (string-append "SUITESPARSE_INC=-I "
 262         ;;                (assoc-ref %build-inputs "suitesparse")
 263         ;;                "/include")
 264
 265         "USE_GPL_LIBS=1"        ;proudly
 266         "USE_SYSTEM_UTF8PROC=1"
 267         (string-append "UTF8PROC_INC="
 268                        (assoc-ref %build-inputs "utf8proc")
 269                        "/include")
 270         "USE_SYSTEM_LLVM=1"
 271         "USE_SYSTEM_LIBUNWIND=1"
 272         "USE_SYSTEM_LIBUV=1"
 273         (string-append "LIBUV="
 274                        (assoc-ref %build-inputs "libuv")
 275                        "/lib/libuv.so")
 276         (string-append "LIBUV_INC="
 277                        (assoc-ref %build-inputs "libuv")
 278                        "/include")
 279         "USE_SYSTEM_PATCHELF=1"
 280         "USE_SYSTEM_PCRE=1"
 281         "USE_SYSTEM_OPENLIBM=1"
 282         "USE_SYSTEM_GMP=1"
 283         "USE_SYSTEM_MPFR=1"
 284         "USE_SYSTEM_ARPACK=1"
 285         "USE_SYSTEM_LIBGIT2=1"
 286         "USE_SYSTEM_OPENSPECFUN=1")))
 287     (inputs
 288      `(("llvm" ,llvm)
 289        ("arpack-ng" ,arpack-ng)
 290        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
 291        ("lapack" ,lapack)
 292        ("openblas" ,openblas) ;Julia does not build with Atlas
 293        ("libunwind" ,libunwind-for-julia)
 294        ("openlibm" ,openlibm)
 295        ("openspecfun" ,openspecfun)
 296        ("libgit2" ,libgit2)
 297        ("fftw" ,fftw)
 298        ("fftwf" ,fftwf)
 299        ("fortran" ,gfortran)
 300        ("libuv" ,libuv-julia)
 301        ("pcre2" ,pcre2)
 302        ("utf8proc" ,utf8proc)
 303        ("mpfr" ,mpfr)
 304        ("wget" ,wget)
 305        ("which" ,which)
 306        ("zlib" ,zlib)
 307        ("gmp" ,gmp)
 308        ("virtualenv" ,python2-virtualenv)
 309        ;; FIXME: The following inputs are downloaded from upstream to allow us
 310        ;; to use the lightweight Julia release tarball.  Ideally, these inputs
 311        ;; would eventually be replaced with proper Guix packages.
 312
 313        ;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
 314        ("suitesparse"
 315         ,(origin
 316            (method url-fetch)
 317            (uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
 318            (sha256
 319             (base32
 320              "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
 321        ("objconv"
 322         ,(origin
 323            (method url-fetch)
 324            (uri "http://www.agner.org/optimize/objconv.zip")
 325            (sha256
 326             (base32
 327              "1fi7qa2sd9vb35dvkgripjf0fayzg2qmff215f8agfqfiwd1g8qs"))))
 328        ("dsfmt"
 329         ,(origin
 330            (method url-fetch)
 331            (uri (string-append
 332                  "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
 333                  "SFMT/dSFMT-src-2.2.3.tar.gz"))
 334            (sha256
 335             (base32
 336              "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
 337     (native-inputs
 338      `(("openssl" ,openssl)
 339        ("perl" ,perl)
 340        ("patchelf" ,patchelf)
 341        ("pkg-config" ,pkg-config)
 342        ("python" ,python-2)))
 343     ;; Julia is not officially released for ARM and MIPS.
 344     ;; See https://github.com/JuliaLang/julia/issues/10639
 345     (supported-systems '("i686-linux" "x86_64-linux"))
 346     (home-page "http://julialang.org/")
 347     (synopsis "High-performance dynamic language for technical computing")
 348     (description
 349      "Julia is a high-level, high-performance dynamic programming language for
 350 technical computing, with syntax that is familiar to users of other technical
 351 computing environments.  It provides a sophisticated compiler, distributed
 352 parallel execution, numerical accuracy, and an extensive mathematical function
 353 library.")
 354     (license license:expat)))