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 ;;; Copyright © 2020 Tim Howes <timhowes@lavabit.com>
   6 ;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr>
   7 ;;;
   8 ;;; This file is part of GNU Guix.
   9 ;;;
  10 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  11 ;;; under the terms of the GNU General Public License as published by
  12 ;;; the Free Software Foundation; either version 3 of the License, or (at
  13 ;;; your option) any later version.
  14 ;;;
  15 ;;; GNU Guix is distributed in the hope that it will be useful, but
  16 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  17 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18 ;;; GNU General Public License for more details.
  19 ;;;
  20 ;;; You should have received a copy of the GNU General Public License
  21 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  22
  23 (define-module (gnu packages julia)
  24   #:use-module ((guix licenses) #:prefix license:)
  25   #:use-module (guix packages)
  26   #:use-module (guix download)
  27   #:use-module (guix utils)
  28   #:use-module (guix git-download)
  29   #:use-module (guix build-system gnu)
  30   #:use-module (gnu packages)
  31   #:use-module (gnu packages algebra)
  32   #:use-module (gnu packages base)
  33   #:use-module (gnu packages compression)
  34   #:use-module (gnu packages curl)
  35   #:use-module (gnu packages elf)
  36   #:use-module (gnu packages gcc)
  37   #:use-module (gnu packages llvm)
  38   #:use-module (gnu packages libevent)
  39   #:use-module (gnu packages libunwind)
  40   #:use-module (gnu packages maths)
  41   #:use-module (gnu packages multiprecision) ; mpfr
  42   #:use-module (gnu packages pcre)
  43   #:use-module (gnu packages perl)
  44   #:use-module (gnu packages pkg-config)
  45   #:use-module (gnu packages python)
  46   #:use-module (gnu packages python-xyz)
  47   #:use-module (gnu packages textutils)
  48   #:use-module (gnu packages ssh)
  49   #:use-module (gnu packages tls)
  50   #:use-module (gnu packages version-control)
  51   #:use-module (gnu packages wget)
  52   #:use-module (ice-9 match))
  53
  54 (define libuv-julia
  55   (let ((commit "1fcc6d66f9df74189c74d3d390f02202bb7db953")
  56         (revision "2"))
  57     ;; When upgrading Julia, also upgrade this.  Get the commit from
  58     ;; https://github.com/JuliaLang/julia/blob/v1.5.2/deps/libuv.version
  59     (package
  60       (inherit libuv)
  61       (name "libuv-julia")
  62       (version (git-version "2.0.0" revision commit))
  63       (source (origin
  64                 (method git-fetch)
  65                 (uri (git-reference
  66                        (url "https://github.com/JuliaLang/libuv")
  67                        (commit commit)))
  68                 (file-name (string-append name "-" version "-checkout"))
  69                 (sha256
  70                  (base32
  71                   "040l7f1hk7xyza11sry5cj4fhw05na949865axqqhxnifdvnmfji"))))
  72       (build-system gnu-build-system)
  73       (arguments
  74        (substitute-keyword-arguments (package-arguments libuv)
  75          ((#:phases phases)
  76           `(modify-phases ,phases
  77              (delete 'autogen)))))
  78       (home-page "https://github.com/JuliaLang/libuv"))))
  79
  80 (define libunwind-julia
  81   ;; The Julia projects requires their patched version.
  82   ;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
  83   (package
  84     (inherit libunwind)
  85     (name "libunwind-julia")
  86     (version "1.3.1")
  87     (source
  88      (origin
  89        (method url-fetch)
  90        (uri (string-append "mirror://savannah/libunwind/libunwind-"
  91                            version ".tar.gz"))
  92        (sha256
  93         (base32
  94          "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
  95        (patches
  96         (list
  97          (julia-patch "libunwind-prefer-extbl"
  98                       "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
  99          (julia-patch "libunwind-static-arm"
 100                       "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
 101     (home-page "https://github.com/JuliaLang/tree/master/deps/")))
 102
 103 (define (julia-patch-url version name)
 104   (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
 105                  "/deps/patches/" name ".patch"))
 106
 107 (define (julia-patch name sha)
 108   (let ((version "1.5.3"))
 109     (origin (method url-fetch)
 110             (uri (julia-patch-url version name))
 111             (sha256 (base32 sha))
 112             (file-name name))))
 113
 114 (define llvm-julia
 115   (package
 116     (inherit llvm-9)
 117     (name "llvm-julia")
 118     (source (origin
 119               (inherit (package-source llvm-9))
 120               ;; Those patches are inside the Julia source repo.
 121               ;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
 122               ;; but they are required to build Julia.
 123               ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
 124               (patches
 125                (map (match-lambda
 126                       ((name hash)
 127                        (julia-patch name hash)))
 128                     (list
 129                      '("llvm-D27629-AArch64-large_model_6.0.1"
 130                        "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
 131                      '("llvm8-D34078-vectorize-fdiv"
 132                        "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602")
 133                      '("llvm-7.0-D44650"
 134                        "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir")
 135                      '("llvm9-D50010-VNCoercion-ni"
 136                        "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx")
 137                      '("llvm-exegesis-mingw"
 138                        "0ph1cj1j7arvf1xq2xcr7qf9g0cpdl14fincgr67vpi520zvd3vp")
 139                      '("llvm-test-plugin-mingw"
 140                        "12z738cnahbf6n381im7i0hxp1m6k9hrnfjlmq9sac46nxly9gnj")
 141                      '("llvm7-revert-D44485"
 142                        "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n")
 143                      '("llvm-8.0-D66657-codegen-degenerate"
 144                        "1n1ddx19h90bbpimdyd9dh8fsm6gb93xxyqm4ljkxa1k3cx2vm72")
 145                      '("llvm-8.0-D71495-vectorize-freduce"
 146                        "1zff08wvji9lnpskk4b3p5zyjsy5hhy23ynxjqlj9dw7jvvfrf0p")
 147                      '("llvm-D75072-SCEV-add-type"
 148                        "029a3fywsm233vf48mscina24idd50dc75wr70lmimrhwnw27p0z")
 149                      '("llvm-9.0-D65174-limit-merge-stores"
 150                        "04bff1mnblfj9mxfdwr1qdnw3i3szmp60gnhxwas5y68qg33z6j0")
 151                      '("llvm9-D71443-PPC-MC-redef-symbol"
 152                        "1c93nv7rgc9jg5mqrnvv08xib1789qvlql94fwggh18mp3b9hbgy")
 153                      '("llvm-9.0-D78196"
 154                        "08a43hyg7yyqjq2vmfsmppf34xcz60wq6y9zw5fdyhw2h1mcnmns")
 155                      '("llvm-julia-tsan-custom-as"
 156                        "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s")
 157                      '("llvm-9.0-D85499"
 158                        "0vxlr35srvbvihlgrxq15v6dylp90vgi0qahj22j01jgqmdasjkm"))))
 159               (patch-flags '("-p1"))))
 160     (arguments
 161      (substitute-keyword-arguments (package-arguments llvm-9)
 162        ((#:configure-flags flags)
 163         `(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
 164            "-DCMAKE_BUILD_TYPE=Release"
 165
 166            ;; Build a native compiler and the NVPTX backend (NVIDIA) since
 167            ;; Julia insists on it, nothing more.  This reduces build times and
 168            ;; disk usage.
 169            ,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target))
 170            "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX"
 171
 172            "-DLLVM_INSTALL_UTILS=ON"
 173            "-DLLVM_BUILD_TESTS=ON"
 174            "-DLLVM_ENABLE_FFI=ON"
 175            "-DLLVM_ENABLE_RTTI=ON"
 176            ;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
 177            ;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
 178            ;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
 179            "-DLLVM_ENABLE_DUMP=ON"
 180            "-DLLVM_LINK_LLVM_DYLIB=ON"))))))
 181
 182 (define-public libwhich
 183   (package
 184     (name "libwhich")
 185     (version "1.1.0")
 186     (source
 187      (origin
 188        (method git-fetch)
 189        (uri (git-reference
 190              (url "https://github.com/vtjnash/libwhich")
 191              ;; fixes linux-vdso.so related tests
 192              (commit "87cffe10080c98e7b5786c5166e420bf1ada1d41")))
 193        (file-name (string-append name "-" version "-checkout"))
 194        (sha256
 195         (base32
 196          "1bpa0fcqpa3ai3hm8mz0p13bf76fsq53wsfcx5qw302zh22108xr"))))
 197     (arguments
 198      `(#:make-flags
 199        (list (string-append "CC=" ,(cc-for-target)))
 200        #:phases
 201        (modify-phases %standard-phases
 202          (delete 'configure)
 203          (add-before 'check 'set-ld-library-path
 204            (lambda* (#:key native-inputs inputs #:allow-other-keys)
 205              (setenv "LD_LIBRARY_PATH"
 206                      (string-append (assoc-ref (or native-inputs inputs) "zlib")
 207                                     "/lib"))))
 208          (replace 'install
 209            (lambda* (#:key outputs #:allow-other-keys)
 210              (let ((out (assoc-ref outputs "out")))
 211                (install-file "libwhich" (string-append out "/bin")))
 212              #t)))))
 213     (native-inputs
 214      ;; used for tests
 215      `(("zlib" ,zlib)))
 216     (build-system gnu-build-system)
 217     (home-page "https://github.com/vtjnash/libwhich")
 218     (synopsis "Like @code{which}, for dynamic libraries")
 219     (description "@code{libwhich} is like @code{which}, but for dynamic
 220 libraries.  It is also a bit like @code{ldd} and @code{otool -L}.")
 221     (license license:expat)))
 222
 223 (define-public julia
 224   (package
 225     (name "julia")
 226     (version "1.5.3")
 227     (source (origin
 228               (method url-fetch)
 229               (uri (string-append
 230                     "https://github.com/JuliaLang/julia/releases/download/v"
 231                     version "/julia-" version ".tar.gz"))
 232               (sha256
 233                (base32
 234                 "1zmim82x9kkdcgn0cdi01hmzi59zbszy1sqlygb86xq4hc1n66dy"))
 235               (patches
 236                (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
 237     (build-system gnu-build-system)
 238     (arguments
 239      `(#:test-target "test"
 240        #:modules ((ice-9 match)
 241                   (guix build gnu-build-system)
 242                   (guix build utils))
 243
 244        ;; Do not strip binaries to keep support for full backtraces.
 245        ;; See https://github.com/JuliaLang/julia/issues/17831
 246        #:strip-binaries? #f
 247
 248        ;; The DSOs use $ORIGIN to refer to each other, but (guix build
 249        ;; gremlin) doesn't support it yet, so skip this phase.
 250        #:validate-runpath? #f
 251
 252        #:phases
 253        (modify-phases %standard-phases
 254          (delete 'configure)
 255          (add-after 'unpack 'prepare-deps
 256            (lambda* (#:key inputs #:allow-other-keys)
 257              ;; needed by libwhich
 258              (setenv "LD_LIBRARY_PATH"
 259                      (string-join (map (lambda (pkg)
 260                                          (string-append (assoc-ref inputs pkg)
 261                                                         "/lib"))
 262                                        '("arpack-ng" "curl" "dsfmt"
 263                                          "gmp" "lapack"
 264                                          "libssh2" "libgit2"
 265                                          "mbedtls" "mpfr"
 266                                          "openblas" "openlibm" "pcre2"
 267                                          "suitesparse"))
 268                                   ":"))
 269              #t))
 270          ;; FIXME: Building the documentation requires Julia packages that
 271          ;; would be downloaded from the Internet.  We should build them in a
 272          ;; separate build phase.
 273          (add-after 'unpack 'disable-documentation
 274            (lambda _
 275              (substitute* "Makefile"
 276                (("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
 277                 (string-append line "\n"))
 278                (("src ui doc deps")
 279                 "src ui deps"))
 280              #t))
 281          (add-after 'unpack 'use-system-libwhich
 282            (lambda* (#:key inputs #:allow-other-keys)
 283              ;; don't build it
 284              (substitute* "deps/Makefile"
 285                (("DEP_LIBS \\+= libwhich") ""))
 286              ;; call our version
 287              (substitute* "base/Makefile"
 288                (("\\$\\$\\(build_depsbindir\\)/libwhich")
 289                 (string-append (assoc-ref inputs "libwhich") "/bin/libwhich")))
 290              #t))
 291          (add-before 'check 'set-home
 292            ;; Some tests require a home directory to be set.
 293            (lambda _ (setenv "HOME" "/tmp") #t))
 294          (add-before 'build 'fix-include-and-link-paths
 295            (lambda* (#:key inputs #:allow-other-keys)
 296              ;; LIBUTF8PROC is a linker flag, not a build target.  It is
 297              ;; included in the LIBFILES_* variable which is used as a
 298              ;; collection of build targets and a list of libraries to link
 299              ;; against.
 300              (substitute* "src/flisp/Makefile"
 301                (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
 302                 "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
 303                (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
 304                 "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
 305
 306              ;; The REPL must be linked with libuv.
 307              (substitute* "ui/Makefile"
 308                (("JLDFLAGS \\+= ")
 309                 (string-append "JLDFLAGS += "
 310                                (assoc-ref %build-inputs "libuv")
 311                                "/lib/libuv.so ")))
 312
 313              (substitute* "base/Makefile"
 314                (("\\$\\(build_includedir\\)/uv/errno.h")
 315                 (string-append (assoc-ref inputs "libuv")
 316                                "/include/uv/errno.h")))
 317              #t))
 318          (add-before 'build 'replace-default-shell
 319            (lambda _
 320              (substitute* "base/client.jl"
 321                (("/bin/sh") (which "sh")))
 322              #t))
 323          (add-before 'build 'fix-precompile
 324            (lambda _
 325              (substitute* "base/loading.jl"
 326                (("something(Base.active_project(), \"\")") "\"\""))
 327              #t))
 328          (add-before 'check 'disable-broken-tests
 329            (lambda _
 330              (substitute* "test/choosetests.jl"
 331                (("tests = testnames")
 332                 ;; Those failings are not deterministic.  They depends on the
 333                 ;; running order.  I think it depends on the number of
 334                 ;; runners, disabling it for now
 335                 ;; https://github.com/JuliaLang/julia/issues/34330
 336                 "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",\"precompile\",
 337                                            \"client\",\"stacktraces\"]),
 338                                        testnames)"))
 339              ;; Marking the test as broken as it's a known bug:
 340              ;; https://github.com/JuliaLang/julia/issues/32377
 341              (substitute* "stdlib/REPL/test/replcompletions.jl"
 342                (("@test count") "@test_broken count"))
 343              ;; Dates has a similar bug:
 344              ;; https://github.com/JuliaLang/julia/issues/34655
 345              (substitute* "stdlib/Dates/test/io.jl"
 346                (("\"Dates.Date") "\"Date")
 347                (("\"Dates.Time") "\"Time"))
 348              ;; Upstream bug I found when packaging
 349              ;; https://github.com/JuliaLang/julia/issues/35785
 350              (substitute* "test/file.jl"
 351                (("@test dirname\\(t\\) == d") "@test_broken dirname(t) == d"))
 352              ;; Deprecation test fails with --depwarn=no
 353              ;; https://github.com/JuliaLang/julia/issues/37673
 354              (substitute* "test/Makefile"
 355                (("./runtests.jl") "--depwarn=error ./runtests.jl"))
 356              #t))
 357          (add-after 'install 'make-wrapper
 358            (lambda* (#:key inputs outputs #:allow-other-keys)
 359              (let* ((out (assoc-ref outputs "out"))
 360                     (bin (string-append out "/bin"))
 361                     (program "julia"))
 362                (with-directory-excursion bin
 363                  (wrap-program program
 364                    `("JULIA_LOAD_PATH" ":" prefix
 365                      ("" "$JULIA_LOAD_PATH")))
 366                  (wrap-program program
 367                    `("JULIA_DEPOT_PATH" ":" prefix
 368                      ("" "$JULIA_DEPOT_PATH"))))
 369                #t))))
 370        #:make-flags
 371        (list
 372         (string-append "prefix=" (assoc-ref %outputs "out"))
 373
 374          ;; Passing the MARCH flag is necessary to build binary substitutes for
 375          ;; the supported architectures.
 376          ,(match (or (%current-target-system)
 377                      (%current-system))
 378                  ("x86_64-linux" "MARCH=x86-64")
 379                  ("i686-linux" "MARCH=pentium4")
 380                  ("aarch64-linux" "MARCH=armv8-a")
 381                  ;; Prevent errors when querying this package on unsupported
 382                  ;; platforms, e.g. when running "guix package --search="
 383                  (_ "MARCH=UNSUPPORTED"))
 384
 385          "CONFIG_SHELL=bash"     ;needed to build bundled libraries
 386          ;; list of "USE_SYSTEM_*" is here:
 387          ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
 388          "USE_SYSTEM_DSFMT=1"
 389          "USE_SYSTEM_P7ZIP=1"
 390          "USE_SYSTEM_LAPACK=1"
 391          "USE_SYSTEM_BLAS=1"
 392          "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
 393          "LIBBLAS=-lopenblas"
 394          "LIBBLASNAME=libopenblas"
 395
 396          "USE_SYSTEM_SUITESPARSE=1"
 397          (string-append "SUITESPARSE_INC=-I "
 398                         (assoc-ref %build-inputs "suitesparse")
 399                         "/include")
 400          "USE_GPL_LIBS=1"        ;proudly
 401          "USE_SYSTEM_UTF8PROC=1"
 402          (string-append "UTF8PROC_INC="
 403                         (assoc-ref %build-inputs "utf8proc")
 404                         "/include")
 405          "USE_SYSTEM_LLVM=1"
 406          "LLVM_VER=9.0.1"
 407
 408          "USE_LLVM_SHLIB=1"
 409          "USE_SYSTEM_LIBUNWIND=1"
 410          "USE_SYSTEM_LIBUV=1"
 411          (string-append "LIBUV="
 412                         (assoc-ref %build-inputs "libuv")
 413                         "/lib/libuv.so")
 414          (string-append "LIBUV_INC="
 415                         (assoc-ref %build-inputs "libuv")
 416                         "/include")
 417          "USE_SYSTEM_PATCHELF=1"
 418          "USE_SYSTEM_PCRE=1"
 419          "USE_SYSTEM_OPENLIBM=1"
 420          "USE_SYSTEM_MBEDTLS=1"
 421          "USE_SYSTEM_LIBSSH2=1"
 422          "USE_SYSTEM_GMP=1"
 423          "USE_SYSTEM_MPFR=1"
 424          "USE_SYSTEM_ARPACK=1"
 425          "USE_SYSTEM_LIBGIT2=1"
 426          "USE_SYSTEM_ZLIB=1")))
 427     (inputs
 428      `(("llvm" ,llvm-julia)
 429        ("p7zip" ,p7zip)
 430        ;; The bundled version is 3.3.0 so stick to that version.  With other
 431        ;; versions, we get test failures in 'linalg/arnoldi' as described in
 432        ;; <https://bugs.gnu.org/30282>.
 433        ("arpack-ng" ,arpack-ng-3.3.0)
 434
 435        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
 436        ("lapack" ,lapack)
 437        ("openblas" ,openblas) ;Julia does not build with Atlas
 438        ("libunwind" ,libunwind-julia)
 439        ("openlibm" ,openlibm)
 440        ("mbedtls" ,mbedtls-apache)
 441        ("curl" ,curl)
 442        ("libgit2" ,libgit2-0.28)
 443        ("libssh2" ,libssh2)
 444        ("fortran" ,gfortran)
 445        ("libuv" ,libuv-julia)
 446        ("pcre2" ,pcre2)
 447        ("utf8proc" ,utf8proc)
 448        ("mpfr" ,mpfr)
 449        ("wget" ,wget)
 450        ("which" ,which)
 451        ("zlib" ,zlib)
 452        ("gmp" ,gmp)
 453        ("suitesparse" ,suitesparse)
 454        ;; Find dependencies versions here:
 455        ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
 456        ("libwhich" ,libwhich)
 457        ("dsfmt" ,dsfmt)))
 458     (native-inputs
 459      `(("openssl" ,openssl)
 460        ("perl" ,perl)
 461        ("patchelf" ,patchelf)
 462        ("pkg-config" ,pkg-config)
 463        ("python" ,python-2)))
 464     (native-search-paths
 465       (list (search-path-specification
 466               (variable "JULIA_LOAD_PATH")
 467               (files (list "share/julia/packages/")))
 468             (search-path-specification
 469               (variable "JULIA_DEPOT_PATH")
 470               (files (list "share/julia/")))))
 471     ;; Julia is not officially released for ARM and MIPS.
 472     ;; See https://github.com/JuliaLang/julia/issues/10639
 473     (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
 474     (home-page "https://julialang.org/")
 475     (synopsis "High-performance dynamic language for technical computing")
 476     (description
 477      "Julia is a high-level, high-performance dynamic programming language for
 478 technical computing, with syntax that is familiar to users of other technical
 479 computing environments.  It provides a sophisticated compiler, distributed
 480 parallel execution, numerical accuracy, and an extensive mathematical function
 481 library.")
 482     (license license:expat)))