gnu/packages/julia.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017 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 python-xyz)
  43   #:use-module (gnu packages textutils)
  44   #:use-module (gnu packages tls)
  45   #:use-module (gnu packages version-control)
  46   #:use-module (gnu packages wget)
  47   #:use-module (ice-9 match))
  48
  49 (define libuv-julia
  50   (let ((commit "52d72a52cc7ccd570929990f010ed16e2ec604c8")
  51         (revision "5"))
  52     (package (inherit libuv)
  53       (name "libuv-julia")
  54       (version (string-append "1.9.0-" revision "." (string-take commit 8)))
  55       (source (origin
  56                 (method git-fetch)
  57                 (uri (git-reference
  58                       (url "https://github.com/JuliaLang/libuv.git")
  59                       (commit commit)))
  60                 (file-name (string-append name "-" version "-checkout"))
  61                 (sha256
  62                  (base32
  63                   "1daxh6ci6q7znxxajr3bm16dd53ragm0d681wf4kzg542qnjq3lh"))))
  64       (build-system gnu-build-system)
  65       (arguments
  66        (substitute-keyword-arguments (package-arguments libuv)
  67          ((#:phases phases)
  68           `(modify-phases ,phases
  69              (delete 'autogen)))))
  70       (home-page "https://github.com/JuliaLang/libuv"))))
  71
  72 (define libunwind-for-julia
  73   (package
  74     (inherit libunwind)
  75     (version "1.1-julia2")
  76     (source (origin
  77               (method url-fetch)
  78               (uri (string-append "https://s3.amazonaws.com/julialang/src/"
  79                                   "libunwind-" version ".tar.gz"))
  80               (sha256
  81                (base32
  82                 "0499x7sg2v18a6cry6l8y713cgmic0adnjph8i0xr1db9p7n8qyv"))))))
  83
  84 (define-public julia
  85   (package
  86     (name "julia")
  87     (version "0.6.0")
  88     (source (origin
  89               (method url-fetch)
  90               (uri (string-append
  91                     "https://github.com/JuliaLang/julia/releases/download/v"
  92                     version "/julia-" version ".tar.gz"))
  93               (sha256
  94                (base32
  95                 "0rd6lcc9sic10q1j3c6f9qr901i1c4554m93n2sz5b3mh37byqhw"))))
  96     (build-system gnu-build-system)
  97     (arguments
  98      `(#:test-target "test"
  99        #:modules ((ice-9 match)
 100                   (guix build gnu-build-system)
 101                   (guix build utils))
 102
 103        ;; Do not strip binaries to keep support for full backtraces.
 104        ;; See https://github.com/JuliaLang/julia/issues/17831
 105        #:strip-binaries? #f
 106
 107        ;; The DSOs use $ORIGIN to refer to each other, but (guix build
 108        ;; gremlin) doesn't support it yet, so skip this phase.
 109        #:validate-runpath? #f
 110
 111        #:phases
 112        (modify-phases %standard-phases
 113          (delete 'configure)
 114          (add-after 'unpack 'prepare-deps
 115            (lambda* (#:key inputs #:allow-other-keys)
 116              (mkdir "deps/srccache")
 117              (copy-file (assoc-ref inputs "dsfmt")
 118                         "deps/srccache/dsfmt-2.2.3.tar.gz")
 119              (copy-file (assoc-ref inputs "objconv")
 120                         "deps/srccache/objconv.zip")
 121              (copy-file (assoc-ref inputs "suitesparse")
 122                         "deps/srccache/SuiteSparse-4.4.5.tar.gz")
 123              (copy-file (string-append (assoc-ref inputs "virtualenv")
 124                                        "/bin/virtualenv")
 125                         "julia-env")
 126              (copy-file (assoc-ref inputs "unicode-data")
 127                         "doc/UnicodeData.txt")
 128              #t))
 129          ;; FIXME: Building the documentation requires Julia packages that
 130          ;; would be downloaded from the Internet.  We should build them in a
 131          ;; separate build phase.
 132          (add-after 'unpack 'disable-documentation
 133            (lambda _
 134              (substitute* "Makefile"
 135                (("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
 136                 (string-append line "\n"))
 137                (("src ui doc deps")
 138                 "src ui deps"))
 139              #t))
 140          (add-before 'check 'set-home
 141            ;; Some tests require a home directory to be set.
 142            (lambda _ (setenv "HOME" "/tmp") #t))
 143          (add-after 'unpack 'hardcode-soname-map
 144           ;; ./src/runtime_ccall.cpp creates a map from library names to paths
 145           ;; using the output of "/sbin/ldconfig -p".  Since ldconfig is not
 146           ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
 147           (lambda* (#:key inputs #:allow-other-keys)
 148             (use-modules (ice-9 match))
 149             (substitute* "src/runtime_ccall.cpp"
 150               ;; Patch out invocations of '/sbin/ldconfig' to avoid getting
 151               ;; error messages about missing '/sbin/ldconfig' on Guix System.
 152               (("popen\\(.*ldconfig.*\\);")
 153                "NULL;\n")
 154
 155               ;; Populate 'sonameMap'.
 156               (("jl_read_sonames.*;")
 157                (string-join
 158                 (map (match-lambda
 159                        ((input libname soname)
 160                         (string-append
 161                          "sonameMap[\"" libname "\"] = "
 162                          "\"" (assoc-ref inputs input) "/lib/" soname "\";")))
 163                      '(("libc"        "libc"           "libc.so.6")
 164                        ("pcre2"       "libpcre2-8"     "libpcre2-8.so")
 165                        ("mpfr"        "libmpfr"        "libmpfr.so")
 166                        ("openblas"    "libblas"        "libopenblas.so")
 167                        ("arpack-ng"   "libarpack"      "libarpack.so")
 168                        ("lapack"      "liblapack"      "liblapack.so")
 169                        ("libgit2"     "libgit2"        "libgit2.so")
 170                        ("gmp"         "libgmp"         "libgmp.so")
 171                        ("openlibm"    "libopenlibm"    "libopenlibm.so")
 172                        ("openspecfun" "libopenspecfun" "libopenspecfun.so")
 173                        ("fftw"        "libfftw3"       "libfftw3_threads.so")
 174                        ("fftwf"       "libfftw3f"      "libfftw3f_threads.so"))))))
 175             (substitute* "base/fft/FFTW.jl"
 176               (("const libfftw = Base.libfftw_name")
 177                (string-append "const libfftw = \""
 178                               (assoc-ref inputs "fftw") "/lib/libfftw3_threads.so"
 179                               "\""))
 180               (("const libfftwf = Base.libfftwf_name")
 181                (string-append "const libfftwf = \""
 182                               (assoc-ref inputs "fftwf") "/lib/libfftw3f_threads.so"
 183                               "\"")))
 184             (substitute* "base/math.jl"
 185               (("const libm = Base.libm_name")
 186                (string-append "const libm = \""
 187                               (assoc-ref inputs "openlibm")
 188                               "/lib/libopenlibm.so"
 189                               "\""))
 190               (("const openspecfun = \"libopenspecfun\"")
 191                (string-append "const openspecfun = \""
 192                               (assoc-ref inputs "openspecfun")
 193                               "/lib/libopenspecfun.so"
 194                               "\"")))
 195             (substitute* "base/pcre.jl"
 196               (("const PCRE_LIB = \"libpcre2-8\"")
 197                (string-append "const PCRE_LIB = \""
 198                               (assoc-ref inputs "pcre2")
 199                               "/lib/libpcre2-8.so" "\"")))
 200             #t))
 201          (add-before 'build 'fix-include-and-link-paths
 202           (lambda* (#:key inputs #:allow-other-keys)
 203             ;; LIBUTF8PROC is a linker flag, not a build target.  It is
 204             ;; included in the LIBFILES_* variable which is used as a
 205             ;; collection of build targets and a list of libraries to link
 206             ;; against.
 207             (substitute* "src/flisp/Makefile"
 208               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
 209                "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
 210               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
 211                "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
 212
 213             ;; The REPL must be linked with libuv.
 214             (substitute* "ui/Makefile"
 215               (("JLDFLAGS \\+= ")
 216                (string-append "JLDFLAGS += "
 217                               (assoc-ref %build-inputs "libuv")
 218                               "/lib/libuv.so ")))
 219
 220             (substitute* "base/Makefile"
 221               (("\\$\\(build_includedir\\)/uv-errno.h")
 222                (string-append (assoc-ref inputs "libuv")
 223                               "/include/uv-errno.h")))
 224             #t))
 225          (add-before 'build 'replace-default-shell
 226           (lambda _
 227             (substitute* "base/client.jl"
 228               (("/bin/sh") (which "sh")))
 229             #t))
 230          (add-after 'unpack 'hardcode-paths
 231            (lambda _
 232              (substitute* "base/interactiveutil.jl"
 233                (("`which") (string-append "`" (which "which")))
 234                (("`wget")  (string-append "`" (which "wget"))))
 235              #t))
 236          (add-before 'check 'disable-broken-tests
 237            (lambda _
 238              ;; Adjust expected error messages to match what current libgit2
 239              ;; provides.
 240              (substitute* "test/libgit2.jl"
 241                (("Invalid Content-Type") "invalid Content-Type")
 242                (("Failed to resolve path") "failed to resolve path"))
 243
 244              (substitute* "test/choosetests.jl"
 245                ;; These tests fail, probably because some of the input
 246                ;; binaries have been stripped and thus backtraces don't look
 247                ;; as expected.
 248                (("\"backtrace\",") "")
 249                (("\"compile\",") "")
 250                (("\"replutil\",") "")
 251                (("\"cmdlineargs\",") "")
 252                ;; FIXME: This test fails with the following error:
 253                ;; Error in testset file:
 254                ;; Test Failed
 255                ;;   Expression: download("ba\0d", "good")
 256                ;;     Expected: ArgumentError
 257                ;;       Thrown: Base.UVError
 258                (("\"file\",") ""))
 259              #t)))
 260        #:make-flags
 261        (list
 262         (string-append "prefix=" (assoc-ref %outputs "out"))
 263
 264         ;; Passing the MARCH flag is necessary to build binary substitutes for
 265         ;; the supported architectures.
 266         ,(match (or (%current-target-system)
 267                     (%current-system))
 268            ("x86_64-linux" "MARCH=x86-64")
 269            ("i686-linux" "MARCH=pentium4")
 270            ("aarch64-linux" "MARCH=armv8-a")
 271            ;; Prevent errors when querying this package on unsupported
 272            ;; platforms, e.g. when running "guix package --search="
 273            (_ "MARCH=UNSUPPORTED"))
 274
 275         "CONFIG_SHELL=bash"     ;needed to build bundled libraries
 276         "USE_SYSTEM_DSFMT=0"    ;not packaged for Guix and upstream has no
 277                                 ;build system for a shared library.
 278         "USE_SYSTEM_LAPACK=1"
 279         "USE_SYSTEM_BLAS=1"
 280         "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
 281
 282         "USE_SYSTEM_FFTW=1"
 283         "LIBFFTWNAME=libfftw3"
 284         "LIBFFTWFNAME=libfftw3f"
 285
 286         ;; TODO: Suitesparse does not install shared libraries, so we cannot
 287         ;; use the suitesparse package.
 288         ;; "USE_SYSTEM_SUITESPARSE=1"
 289         ;; (string-append "SUITESPARSE_INC=-I "
 290         ;;                (assoc-ref %build-inputs "suitesparse")
 291         ;;                "/include")
 292
 293         "USE_GPL_LIBS=1"        ;proudly
 294         "USE_SYSTEM_UTF8PROC=1"
 295         (string-append "UTF8PROC_INC="
 296                        (assoc-ref %build-inputs "utf8proc")
 297                        "/include")
 298         "USE_SYSTEM_LLVM=1"
 299         "USE_LLVM_SHLIB=0" ; FIXME: fails when set to 1
 300
 301         "USE_SYSTEM_LIBUNWIND=1"
 302         "USE_SYSTEM_LIBUV=1"
 303         (string-append "LIBUV="
 304                        (assoc-ref %build-inputs "libuv")
 305                        "/lib/libuv.so")
 306         (string-append "LIBUV_INC="
 307                        (assoc-ref %build-inputs "libuv")
 308                        "/include")
 309         "USE_SYSTEM_PATCHELF=1"
 310         "USE_SYSTEM_PCRE=1"
 311         "USE_SYSTEM_OPENLIBM=1"
 312         "USE_SYSTEM_GMP=1"
 313         "USE_SYSTEM_MPFR=1"
 314         "USE_SYSTEM_ARPACK=1"
 315         "USE_SYSTEM_LIBGIT2=1"
 316         "USE_SYSTEM_OPENSPECFUN=1")))
 317     (inputs
 318      `(("llvm" ,llvm-3.9.1)
 319
 320        ;; The bundled version is 3.3.0 so stick to that version.  With other
 321        ;; versions, we get test failures in 'linalg/arnoldi' as described in
 322        ;; <https://bugs.gnu.org/30282>.
 323        ("arpack-ng" ,arpack-ng-3.3.0)
 324
 325        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
 326        ("lapack" ,lapack)
 327        ("openblas" ,openblas) ;Julia does not build with Atlas
 328        ("libunwind" ,libunwind-for-julia)
 329        ("openlibm" ,openlibm)
 330        ("openspecfun" ,openspecfun)
 331        ("libgit2" ,libgit2)
 332        ("fftw" ,fftw)
 333        ("fftwf" ,fftwf)
 334        ("fortran" ,gfortran)
 335        ("libuv" ,libuv-julia)
 336        ("pcre2" ,pcre2)
 337        ("utf8proc" ,utf8proc)
 338        ("mpfr" ,mpfr)
 339        ("wget" ,wget)
 340        ("which" ,which)
 341        ("zlib" ,zlib)
 342        ("gmp" ,gmp)
 343        ("virtualenv" ,python2-virtualenv)
 344        ;; FIXME: The following inputs are downloaded from upstream to allow us
 345        ;; to use the lightweight Julia release tarball.  Ideally, these inputs
 346        ;; would eventually be replaced with proper Guix packages.
 347
 348        ;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
 349        ("suitesparse"
 350         ,(origin
 351            (method url-fetch)
 352            (uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
 353            (sha256
 354             (base32
 355              "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
 356        ("objconv"
 357         ,(origin
 358            (method url-fetch)
 359            ;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
 360            (uri "https://www.agner.org/optimize/objconv.zip")
 361            (file-name "objconv-2018-10-07.zip")
 362            (sha256
 363             (base32
 364              "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
 365        ("dsfmt"
 366         ,(origin
 367            (method url-fetch)
 368            (uri (string-append
 369                  "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
 370                  "SFMT/dSFMT-src-2.2.3.tar.gz"))
 371            (sha256
 372             (base32
 373              "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
 374     (native-inputs
 375      `(("openssl" ,openssl)
 376        ("perl" ,perl)
 377        ("patchelf" ,patchelf)
 378        ("pkg-config" ,pkg-config)
 379        ("python" ,python-2)
 380        ("unicode-data"
 381         ,(origin
 382            (method url-fetch)
 383            (uri "http://www.unicode.org/Public/9.0.0/ucd/UnicodeData.txt")
 384            (sha256
 385             (base32
 386              "13zfannnr6sa6s27ggvcvzmh133ndi38pfyxsssvjmw2s8ac9pv8"))))))
 387     ;; Julia is not officially released for ARM and MIPS.
 388     ;; See https://github.com/JuliaLang/julia/issues/10639
 389     (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
 390     (home-page "https://julialang.org/")
 391     (synopsis "High-performance dynamic language for technical computing")
 392     (description
 393      "Julia is a high-level, high-performance dynamic programming language for
 394 technical computing, with syntax that is familiar to users of other technical
 395 computing environments.  It provides a sophisticated compiler, distributed
 396 parallel execution, numerical accuracy, and an extensive mathematical function
 397 library.")
 398     (license license:expat)))