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, 2020 Efraim Flashner <efraim@flashner.co.il>
   4 ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
   5 ;;;
   6 ;;; This file is part of GNU Guix.
   7 ;;;
   8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   9 ;;; under the terms of the GNU General Public License as published by
  10 ;;; the Free Software Foundation; either version 3 of the License, or (at
  11 ;;; your option) any later version.
  12 ;;;
  13 ;;; GNU Guix is distributed in the hope that it will be useful, but
  14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  16 ;;; GNU General Public License for more details.
  17 ;;;
  18 ;;; You should have received a copy of the GNU General Public License
  19 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  20
  21 (define-module (gnu packages julia)
  22   #:use-module ((guix licenses) #:prefix license:)
  23   #:use-module (guix packages)
  24   #:use-module (guix download)
  25   #:use-module (guix utils)
  26   #:use-module (guix git-download)
  27   #:use-module (guix build-system gnu)
  28   #:use-module (gnu packages)
  29   #:use-module (gnu packages algebra)
  30   #:use-module (gnu packages base)
  31   #:use-module (gnu packages compression)
  32   #:use-module (gnu packages curl)
  33   #:use-module (gnu packages elf)
  34   #:use-module (gnu packages gcc)
  35   #:use-module (gnu packages llvm)
  36   #:use-module (gnu packages libevent)
  37   #:use-module (gnu packages libunwind)
  38   #:use-module (gnu packages maths)
  39   #:use-module (gnu packages multiprecision) ; mpfr
  40   #:use-module (gnu packages pcre)
  41   #:use-module (gnu packages perl)
  42   #:use-module (gnu packages pkg-config)
  43   #:use-module (gnu packages python)
  44   #:use-module (gnu packages python-xyz)
  45   #:use-module (gnu packages textutils)
  46   #:use-module (gnu packages ssh)
  47   #:use-module (gnu packages tls)
  48   #:use-module (gnu packages version-control)
  49   #:use-module (gnu packages wget)
  50   #:use-module (ice-9 match))
  51
  52 (define libuv-julia
  53   (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")
  54         (revision "1"))
  55     ;; When upgrading Julia, also upgrade this.  Get the commit from
  56     ;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
  57     (package
  58       (inherit libuv)
  59       (name "libuv-julia")
  60       (version (git-version "2.0.0" revision commit))
  61       (source (origin
  62                 (method git-fetch)
  63                 (uri (git-reference
  64                        (url "https://github.com/JuliaLang/libuv.git")
  65                        (commit commit)))
  66                 (file-name (string-append name "-" version "-checkout"))
  67                 (sha256
  68                  (base32
  69                   "0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
  70       (build-system gnu-build-system)
  71       (arguments
  72        (substitute-keyword-arguments (package-arguments libuv)
  73          ((#:phases phases)
  74           `(modify-phases ,phases
  75              (delete 'autogen)))))
  76       (home-page "https://github.com/JuliaLang/libuv"))))
  77
  78 (define libunwind-julia
  79   ;; The Julia projects requires their patched version.
  80   ;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
  81   (package
  82     (inherit libunwind)
  83     (name "libunwind-julia")
  84     (version "1.3.1")
  85     (source
  86      (origin
  87        (method url-fetch)
  88        (uri (string-append "mirror://savannah/libunwind/libunwind-"
  89                            version ".tar.gz"))
  90        (sha256
  91         (base32
  92          "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
  93        (patches
  94         (list
  95          (julia-patch "libunwind-prefer-extbl"
  96                       "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
  97          (julia-patch "libunwind-static-arm"
  98                       "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
  99     (home-page "https://github.com/JuliaLang/tree/master/deps/")))
 100
 101 (define (julia-patch-url version name)
 102   (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
 103                  "/deps/patches/" name))
 104
 105 (define (julia-patch name sha)
 106   (let ((version "1.3.1"))
 107     (origin (method url-fetch)
 108             (uri (julia-patch-url version name))
 109             (sha256 (base32 sha))
 110             (file-name name))))
 111
 112 (define llvm-julia
 113   (package
 114     (inherit llvm-6)
 115     (name "llvm-julia")
 116     (source (origin
 117               (inherit (package-source llvm-6))
 118               ;; Those patches are inside the Julia source repo.
 119               ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
 120               ;; but they are required to build Julia.
 121               ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
 122               (patches
 123                 (map (match-lambda
 124                        ((name hash)
 125                         (julia-patch name hash)))
 126                      (list
 127                        '("llvm-6.0-D44650"
 128                          "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
 129                        '("llvm-6.0-DISABLE_ABI_CHECKS"
 130                          "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
 131                        '("llvm-6.0-NVPTX-addrspaces"
 132                          "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
 133                        '("llvm-6.0.0_D27296-libssp"
 134                          "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
 135                        '("llvm-D27629-AArch64-large_model_6.0.1"
 136                          "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
 137                        '("llvm-D34078-vectorize-fdiv"
 138                          "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
 139                        '("llvm-D42262-jumpthreading-not-i1"
 140                          "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
 141                        '("llvm-D44892-Perf-integration"
 142                          "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
 143                        '("llvm-D46460"
 144                          "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
 145                        '("llvm-D49832-SCEVPred"
 146                          "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
 147                        '("llvm-D50010-VNCoercion-ni"
 148                          "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
 149                        '("llvm-D50167-scev-umin"
 150                          "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
 151                        '("llvm-OProfile-line-num"
 152                          "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
 153                        '("llvm-PPC-addrspaces"
 154                          "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
 155                        '("llvm-rL323946-LSRTy"
 156                          "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
 157                        '("llvm-rL326967-aligned-load"
 158                          "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
 159                        '("llvm-rL327898"
 160                          "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))))
 161     (arguments
 162      (substitute-keyword-arguments (package-arguments llvm-6)
 163        ((#:configure-flags flags)
 164         `(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
 165            "-DCMAKE_BUILD_TYPE=Release"
 166
 167            ;; Build a native compiler and the NVPTX backend (NVIDIA) since
 168            ;; Julia insists on it, nothing more.  This reduces build times and
 169            ;; disk usage.
 170            ,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target))
 171            "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX"
 172
 173            "-DLLVM_INSTALL_UTILS=ON"
 174            "-DLLVM_BUILD_TESTS=ON"
 175            "-DLLVM_ENABLE_FFI=ON"
 176            "-DLLVM_ENABLE_RTTI=ON"
 177            ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
 178            ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
 179            ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
 180            "-DLLVM_ENABLE_DUMP=ON"
 181            "-DLLVM_LINK_LLVM_DYLIB=ON"))))))
 182
 183 (define-public julia
 184   (package
 185     (name "julia")
 186     (version "1.3.1")
 187     (source (origin
 188               (method url-fetch)
 189               (uri (string-append
 190                     "https://github.com/JuliaLang/julia/releases/download/v"
 191                     version "/julia-" version ".tar.gz"))
 192               (sha256
 193                (base32
 194                 "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
 195               (patches
 196                (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
 197     (build-system gnu-build-system)
 198     (arguments
 199      `(#:test-target "test"
 200        #:modules ((ice-9 match)
 201                   (guix build gnu-build-system)
 202                   (guix build utils))
 203
 204        ;; Do not strip binaries to keep support for full backtraces.
 205        ;; See https://github.com/JuliaLang/julia/issues/17831
 206        #:strip-binaries? #f
 207
 208        ;; The DSOs use $ORIGIN to refer to each other, but (guix build
 209        ;; gremlin) doesn't support it yet, so skip this phase.
 210        #:validate-runpath? #f
 211
 212        #:phases
 213        (modify-phases %standard-phases
 214          (delete 'configure)
 215          (add-after 'unpack 'prepare-deps
 216            (lambda* (#:key inputs #:allow-other-keys)
 217              (mkdir "deps/srccache")
 218              ;; no USE_SYSTEM_{OBJCONV/LIBWHICH} option
 219              (copy-file (assoc-ref inputs "objconv")
 220                         "deps/srccache/objconv.zip")
 221              (copy-file (assoc-ref inputs "libwhich")
 222                         (string-append "deps/srccache/libwhich-"
 223                                        "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
 224                                        ".tar.gz"))
 225
 226              ;; needed by libwhich
 227              (setenv "LD_LIBRARY_PATH"
 228                      (string-join (map (lambda (pkg)
 229                                          (string-append (assoc-ref inputs pkg)
 230                                                         "/lib"))
 231                                        '("arpack-ng" "curl" "dsfmt"
 232                                          "gmp" "lapack"
 233                                          "libssh2" "libgit2"
 234                                          "mbedtls" "mpfr"
 235                                          "openblas" "openlibm" "pcre2"
 236                                          "suitesparse"))
 237                                   ":"))
 238              #t))
 239          ;; FIXME: Building the documentation requires Julia packages that
 240          ;; would be downloaded from the Internet.  We should build them in a
 241          ;; separate build phase.
 242          (add-after 'unpack 'disable-documentation
 243            (lambda _
 244              (substitute* "Makefile"
 245                (("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
 246                 (string-append line "\n"))
 247                (("src ui doc deps")
 248                 "src ui deps"))
 249              #t))
 250          (add-before 'check 'set-home
 251            ;; Some tests require a home directory to be set.
 252            (lambda _ (setenv "HOME" "/tmp") #t))
 253          (add-after 'unpack 'hardcode-soname-map
 254            ;; ./src/runtime_ccall.cpp creates a map from library names to paths
 255            ;; using the output of "/sbin/ldconfig -p".  Since ldconfig is not
 256            ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
 257            (lambda* (#:key inputs #:allow-other-keys)
 258              (substitute* "base/math.jl"
 259                (("const libm = Base.libm_name")
 260                 (string-append "const libm = \""
 261                                (assoc-ref inputs "openlibm")
 262                                "/lib/libopenlibm.so"
 263                                "\"")))
 264              #t))
 265          (add-before 'build 'fix-include-and-link-paths
 266            (lambda* (#:key inputs #:allow-other-keys)
 267              ;; LIBUTF8PROC is a linker flag, not a build target.  It is
 268              ;; included in the LIBFILES_* variable which is used as a
 269              ;; collection of build targets and a list of libraries to link
 270              ;; against.
 271              (substitute* "src/flisp/Makefile"
 272                (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
 273                 "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
 274                (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
 275                 "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
 276
 277              ;; The REPL must be linked with libuv.
 278              (substitute* "ui/Makefile"
 279                (("JLDFLAGS \\+= ")
 280                 (string-append "JLDFLAGS += "
 281                                (assoc-ref %build-inputs "libuv")
 282                                "/lib/libuv.so ")))
 283
 284              (substitute* "base/Makefile"
 285                (("\\$\\(build_includedir\\)/uv/errno.h")
 286                 (string-append (assoc-ref inputs "libuv")
 287                                "/include/uv/errno.h")))
 288              #t))
 289          (add-before 'build 'replace-default-shell
 290            (lambda _
 291              (substitute* "base/client.jl"
 292                (("/bin/sh") (which "sh")))
 293              #t))
 294          (add-before 'build 'fix-precompile
 295            (lambda _
 296              (substitute* "base/loading.jl"
 297                (("something(Base.active_project(), \"\")") "\"\""))
 298              #t))
 299          (add-before 'check 'disable-broken-tests
 300            (lambda _
 301              (substitute* "test/choosetests.jl"
 302                (("tests = testnames")
 303                 ;; Those failings are not deterministic.  They depends on the
 304                 ;; running order.  I think it depends on the number of
 305                 ;; runners, disabling it for now
 306                 ;; https://github.com/JuliaLang/julia/issues/34330
 307                 "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",
 308                                           \"stress\",\"precompile\",
 309                                           \"client\",\"stacktraces\"]),
 310                                        testnames)"))
 311              ;; When HOME is not set, julia calls uv_os_homedir, which in
 312              ;; turns call getpwuid_r. Add the HOME env variable to the
 313              ;; external julia call to fix this
 314              (substitute* "test/cmdlineargs.jl"
 315                (("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
 316              ;; Marking the test as broken as it's a known bug:
 317              ;; https://github.com/JuliaLang/julia/issues/32377
 318              (substitute* "stdlib/REPL/test/replcompletions.jl"
 319                (("@test count") "@test_broken count"))
 320              #t))
 321        (add-after 'install 'make-wrapper
 322          (lambda* (#:key inputs outputs #:allow-other-keys)
 323            (let* ((out (assoc-ref outputs "out"))
 324                   (bin (string-append out "/bin"))
 325                   (program "julia"))
 326              (with-directory-excursion bin
 327                (wrap-program program
 328                              `("JULIA_LOAD_PATH" ":" prefix
 329                                ("" "$JULIA_LOAD_PATH")))
 330                (wrap-program program
 331                              `("JULIA_DEPOT_PATH" ":" prefix
 332                                ("" "$JULIA_DEPOT_PATH"))))
 333              #t))))
 334        #:make-flags
 335        (list
 336          (string-append "prefix=" (assoc-ref %outputs "out"))
 337          (string-append "PREFIX=" (assoc-ref %outputs "out"))
 338
 339          ;; Passing the MARCH flag is necessary to build binary substitutes for
 340          ;; the supported architectures.
 341          ,(match (or (%current-target-system)
 342                      (%current-system))
 343                  ("x86_64-linux" "MARCH=x86-64")
 344                  ("i686-linux" "MARCH=pentium4")
 345                  ("aarch64-linux" "MARCH=armv8-a")
 346                  ;; Prevent errors when querying this package on unsupported
 347                  ;; platforms, e.g. when running "guix package --search="
 348                  (_ "MARCH=UNSUPPORTED"))
 349
 350          "CONFIG_SHELL=bash"     ;needed to build bundled libraries
 351          ;; list of "USE_SYSTEM_*" is here:
 352          ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
 353          "USE_SYSTEM_DSFMT=1"
 354          "USE_SYSTEM_P7ZIP=1"
 355          "USE_SYSTEM_LAPACK=1"
 356          "USE_SYSTEM_BLAS=1"
 357          "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
 358          "LIBBLAS=-lopenblas"
 359          "LIBBLASNAME=libopenblas"
 360
 361          "USE_SYSTEM_SUITESPARSE=1"
 362          (string-append "SUITESPARSE_INC=-I "
 363                         (assoc-ref %build-inputs "suitesparse")
 364                         "/include")
 365          "USE_GPL_LIBS=1"        ;proudly
 366          "USE_SYSTEM_UTF8PROC=1"
 367          (string-append "UTF8PROC_INC="
 368                         (assoc-ref %build-inputs "utf8proc")
 369                         "/include")
 370          "USE_SYSTEM_LLVM=1"
 371          "LLVM_VER=6.0.1"
 372
 373          "USE_LLVM_SHLIB=1"
 374          "USE_SYSTEM_LIBUNWIND=1"
 375          "USE_SYSTEM_LIBUV=1"
 376          (string-append "LIBUV="
 377                         (assoc-ref %build-inputs "libuv")
 378                         "/lib/libuv.so")
 379          (string-append "LIBUV_INC="
 380                         (assoc-ref %build-inputs "libuv")
 381                         "/include")
 382          "USE_SYSTEM_PATCHELF=1"
 383          "USE_SYSTEM_PCRE=1"
 384          "USE_SYSTEM_OPENLIBM=1"
 385
 386          "USE_SYSTEM_GMP=1"
 387          "USE_SYSTEM_MPFR=1"
 388          "USE_SYSTEM_ARPACK=1"
 389          "USE_SYSTEM_LIBGIT2=1"
 390          (string-append "LIBUV="
 391                         (assoc-ref %build-inputs "libuv")
 392                         "/lib/libuv.so")
 393          (string-append "LIBUV_INC="
 394                         (assoc-ref %build-inputs "libuv")
 395                         "/include")
 396          "USE_SYSTEM_ZLIB=1")))
 397     (inputs
 398      `(("llvm" ,llvm-julia)
 399        ("p7zip" ,p7zip)
 400        ;; The bundled version is 3.3.0 so stick to that version.  With other
 401        ;; versions, we get test failures in 'linalg/arnoldi' as described in
 402        ;; <https://bugs.gnu.org/30282>.
 403        ("arpack-ng" ,arpack-ng-3.3.0)
 404
 405        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
 406        ("lapack" ,lapack)
 407        ("openblas" ,openblas) ;Julia does not build with Atlas
 408        ("libunwind" ,libunwind-julia)
 409        ("openlibm" ,openlibm)
 410        ("mbedtls" ,mbedtls-apache)
 411        ("curl" ,curl)
 412        ("libgit2" ,libgit2-0.28)
 413        ("libssh2" ,libssh2)
 414        ("fortran" ,gfortran)
 415        ("libuv" ,libuv-julia)
 416        ("pcre2" ,pcre2)
 417        ("utf8proc" ,utf8proc)
 418        ("mpfr" ,mpfr)
 419        ("wget" ,wget)
 420        ("which" ,which)
 421        ("zlib" ,zlib)
 422        ("gmp" ,gmp)
 423        ("suitesparse" ,suitesparse)
 424        ;; Find dependencies versions here:
 425        ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
 426        ("objconv"
 427         ,(origin
 428            (method url-fetch)
 429            ;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
 430            (uri "https://www.agner.org/optimize/objconv.zip")
 431            (file-name "objconv-2018-10-07.zip")
 432            (sha256
 433             (base32
 434              "0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
 435        ("libwhich"
 436         ,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"))
 437            (origin
 438              ;; Note: We use a /tarball URL, but that's because Julia's build
 439              ;; system checks the hash of that tarball; thus we can't use
 440              ;; 'git-fetch'.
 441              (method url-fetch)
 442              (uri (string-append
 443                     "https://api.github.com/repos/vtjnash/libwhich/tarball/"
 444                     commit))
 445              (file-name (string-append "libwhich-" (string-take commit 7)
 446                                        ".tar.gz"))
 447              (sha256
 448               (base32
 449                "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
 450        ("dsfmt" ,dsfmt)))
 451     (native-inputs
 452      `(("openssl" ,openssl)
 453        ("perl" ,perl)
 454        ("patchelf" ,patchelf)
 455        ("pkg-config" ,pkg-config)
 456        ("python" ,python-2)))
 457     (native-search-paths
 458       (list (search-path-specification
 459               (variable "JULIA_LOAD_PATH")
 460               (files (list "share/julia/packages/")))
 461             (search-path-specification
 462               (variable "JULIA_DEPOT_PATH")
 463               (files (list "share/julia/")))))
 464     ;; Julia is not officially released for ARM and MIPS.
 465     ;; See https://github.com/JuliaLang/julia/issues/10639
 466     (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
 467     (home-page "https://julialang.org/")
 468     (synopsis "High-performance dynamic language for technical computing")
 469     (description
 470      "Julia is a high-level, high-performance dynamic programming language for
 471 technical computing, with syntax that is familiar to users of other technical
 472 computing environments.  It provides a sophisticated compiler, distributed
 473 parallel execution, numerical accuracy, and an extensive mathematical function
 474 library.")
 475     (license license:expat)))