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guix/gnu/packages/julia.scm

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages julia)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix utils)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#:use-module (gnu packages elf)
#:use-module (gnu packages gcc)
#:use-module (gnu packages llvm)
#:use-module (gnu packages libevent)
#:use-module (gnu packages libunwind)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision) ; mpfr
#:use-module (gnu packages pcre)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages textutils)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
#:use-module (gnu packages version-control)
#:use-module (gnu packages wget)
#:use-module (ice-9 match))
(define libuv-julia
(let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1")
(revision "1"))
;; When upgrading Julia, also upgrade this. Get the commit from
;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
(package
(inherit libuv)
(name "libuv-julia")
(version (git-version "2.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/libuv.git")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
(build-system gnu-build-system)
(arguments
(substitute-keyword-arguments (package-arguments libuv)
((#:phases phases)
`(modify-phases ,phases
(delete 'autogen)))))
(home-page "https://github.com/JuliaLang/libuv"))))
(define libunwind-julia
;; The Julia projects requires their patched version.
;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
(package
(inherit libunwind)
(name "libunwind-julia")
(version "1.3.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://savannah/libunwind/libunwind-"
version ".tar.gz"))
(sha256
(base32
"1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
(patches
(list
(julia-patch "libunwind-prefer-extbl"
"0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
(julia-patch "libunwind-static-arm"
"1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
(home-page "https://github.com/JuliaLang/tree/master/deps/")))
(define (julia-patch-url version name)
(string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
"/deps/patches/" name))
(define (julia-patch name sha)
(let ((version "1.3.1"))
(origin (method url-fetch)
(uri (julia-patch-url version name))
(sha256 (base32 sha))
(file-name name))))
(define llvm-julia
(package
(inherit llvm-6)
(name "llvm-julia")
(source (origin
(inherit (package-source llvm-6))
;; Those patches are inside the Julia source repo.
;; They are _not_ Julia specific (https://github.com/julialang/julia#llvm)
;; but they are required to build Julia.
;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
(patches
(map (match-lambda
((name hash)
(julia-patch name hash)))
(list
'("llvm-6.0-D44650"
"1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
'("llvm-6.0-DISABLE_ABI_CHECKS"
"014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
'("llvm-6.0-NVPTX-addrspaces"
"1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
'("llvm-6.0.0_D27296-libssp"
"0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
'("llvm-D27629-AArch64-large_model_6.0.1"
"1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
'("llvm-D34078-vectorize-fdiv"
"1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
'("llvm-D42262-jumpthreading-not-i1"
"1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
'("llvm-D44892-Perf-integration"
"0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
'("llvm-D46460"
"1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
'("llvm-D49832-SCEVPred"
"0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
'("llvm-D50010-VNCoercion-ni"
"0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
'("llvm-D50167-scev-umin"
"1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
'("llvm-OProfile-line-num"
"1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
'("llvm-PPC-addrspaces"
"1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
'("llvm-rL323946-LSRTy"
"10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
'("llvm-rL326967-aligned-load"
"04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
'("llvm-rL327898"
"15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))))
(arguments
(substitute-keyword-arguments (package-arguments llvm-6)
((#:configure-flags flags)
`(list ;; Taken from NixOS. Only way I could get libLLVM-6.0.so
"-DCMAKE_BUILD_TYPE=Release"
;; Build a native compiler and the NVPTX backend (NVIDIA) since
;; Julia insists on it, nothing more. This reduces build times and
;; disk usage.
,(string-append "-DLLVM_TARGETS_TO_BUILD=" (system->llvm-target))
"-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=NVPTX"
"-DLLVM_INSTALL_UTILS=ON"
"-DLLVM_BUILD_TESTS=ON"
"-DLLVM_ENABLE_FFI=ON"
"-DLLVM_ENABLE_RTTI=ON"
;; "-DLLVM_HOST_TRIPLE=${stdenv.hostPlatform.config}"
;; "-DLLVM_DEFAULT_TARGET_TRIPLE=${stdenv.hostPlatform.config}"
;; "-DLLVM_EXPERIMENTAL_TARGETS_TO_BUILD=WebAssembly"
"-DLLVM_ENABLE_DUMP=ON"
"-DLLVM_LINK_LLVM_DYLIB=ON"))))))
(define-public julia
(package
(name "julia")
(version "1.3.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/JuliaLang/julia/releases/download/v"
version "/julia-" version ".tar.gz"))
(sha256
(base32
"1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
(patches
(search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:modules ((ice-9 match)
(guix build gnu-build-system)
(guix build utils))
;; Do not strip binaries to keep support for full backtraces.
;; See https://github.com/JuliaLang/julia/issues/17831
#:strip-binaries? #f
;; The DSOs use $ORIGIN to refer to each other, but (guix build
;; gremlin) doesn't support it yet, so skip this phase.
#:validate-runpath? #f
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-after 'unpack 'prepare-deps
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "deps/srccache")
;; no USE_SYSTEM_{OBJCONV/LIBWHICH} option
(copy-file (assoc-ref inputs "objconv")
"deps/srccache/objconv.zip")
(copy-file (assoc-ref inputs "libwhich")
(string-append "deps/srccache/libwhich-"
"81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
".tar.gz"))
;; needed by libwhich
(setenv "LD_LIBRARY_PATH"
(string-join (map (lambda (pkg)
(string-append (assoc-ref inputs pkg)
"/lib"))
'("arpack-ng" "curl" "dsfmt"
"gmp" "lapack"
"libssh2" "libgit2"
"mbedtls" "mpfr"
"openblas" "openlibm" "pcre2"
"suitesparse"))
":"))
#t))
;; FIXME: Building the documentation requires Julia packages that
;; would be downloaded from the Internet. We should build them in a
;; separate build phase.
(add-after 'unpack 'disable-documentation
(lambda _
(substitute* "Makefile"
(("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line)
(string-append line "\n"))
(("src ui doc deps")
"src ui deps"))
#t))
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t))
(add-after 'unpack 'hardcode-soname-map
;; ./src/runtime_ccall.cpp creates a map from library names to paths
;; using the output of "/sbin/ldconfig -p". Since ldconfig is not
;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "base/math.jl"
(("const libm = Base.libm_name")
(string-append "const libm = \""
(assoc-ref inputs "openlibm")
"/lib/libopenlibm.so"
"\"")))
#t))
(add-before 'build 'fix-include-and-link-paths
(lambda* (#:key inputs #:allow-other-keys)
;; LIBUTF8PROC is a linker flag, not a build target. It is
;; included in the LIBFILES_* variable which is used as a
;; collection of build targets and a list of libraries to link
;; against.
(substitute* "src/flisp/Makefile"
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
"$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
(("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
"$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
;; The REPL must be linked with libuv.
(substitute* "ui/Makefile"
(("JLDFLAGS \\+= ")
(string-append "JLDFLAGS += "
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so ")))
(substitute* "base/Makefile"
(("\\$\\(build_includedir\\)/uv/errno.h")
(string-append (assoc-ref inputs "libuv")
"/include/uv/errno.h")))
#t))
(add-before 'build 'replace-default-shell
(lambda _
(substitute* "base/client.jl"
(("/bin/sh") (which "sh")))
#t))
(add-before 'build 'fix-precompile
(lambda _
(substitute* "base/loading.jl"
(("something(Base.active_project(), \"\")") "\"\""))
#t))
(add-before 'check 'disable-broken-tests
(lambda _
(substitute* "test/choosetests.jl"
(("tests = testnames")
;; Those failings are not deterministic. They depends on the
;; running order. I think it depends on the number of
;; runners, disabling it for now
;; https://github.com/JuliaLang/julia/issues/34330
"tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",
\"stress\",\"precompile\",
\"client\",\"stacktraces\"]),
testnames)"))
;; When HOME is not set, julia calls uv_os_homedir, which in
;; turns call getpwuid_r. Add the HOME env variable to the
;; external julia call to fix this
(substitute* "test/cmdlineargs.jl"
(("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
;; Marking the test as broken as it's a known bug:
;; https://github.com/JuliaLang/julia/issues/32377
(substitute* "stdlib/REPL/test/replcompletions.jl"
(("@test count") "@test_broken count"))
#t))
(add-after 'install 'make-wrapper
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(program "julia"))
(with-directory-excursion bin
(wrap-program program
`("JULIA_LOAD_PATH" ":" prefix
("" "$JULIA_LOAD_PATH")))
(wrap-program program
`("JULIA_DEPOT_PATH" ":" prefix
("" "$JULIA_DEPOT_PATH"))))
#t))))
#:make-flags
(list
(string-append "prefix=" (assoc-ref %outputs "out"))
(string-append "PREFIX=" (assoc-ref %outputs "out"))
;; Passing the MARCH flag is necessary to build binary substitutes for
;; the supported architectures.
,(match (or (%current-target-system)
(%current-system))
("x86_64-linux" "MARCH=x86-64")
("i686-linux" "MARCH=pentium4")
("aarch64-linux" "MARCH=armv8-a")
;; Prevent errors when querying this package on unsupported
;; platforms, e.g. when running "guix package --search="
(_ "MARCH=UNSUPPORTED"))
"CONFIG_SHELL=bash" ;needed to build bundled libraries
;; list of "USE_SYSTEM_*" is here:
;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
"USE_SYSTEM_DSFMT=1"
"USE_SYSTEM_P7ZIP=1"
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=0" ;needed when USE_SYSTEM_BLAS=1
"LIBBLAS=-lopenblas"
"LIBBLASNAME=libopenblas"
"USE_SYSTEM_SUITESPARSE=1"
(string-append "SUITESPARSE_INC=-I "
(assoc-ref %build-inputs "suitesparse")
"/include")
"USE_GPL_LIBS=1" ;proudly
"USE_SYSTEM_UTF8PROC=1"
(string-append "UTF8PROC_INC="
(assoc-ref %build-inputs "utf8proc")
"/include")
"USE_SYSTEM_LLVM=1"
"LLVM_VER=6.0.1"
"USE_LLVM_SHLIB=1"
"USE_SYSTEM_LIBUNWIND=1"
"USE_SYSTEM_LIBUV=1"
(string-append "LIBUV="
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so")
(string-append "LIBUV_INC="
(assoc-ref %build-inputs "libuv")
"/include")
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_PCRE=1"
"USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_LIBGIT2=1"
(string-append "LIBUV="
(assoc-ref %build-inputs "libuv")
"/lib/libuv.so")
(string-append "LIBUV_INC="
(assoc-ref %build-inputs "libuv")
"/include")
"USE_SYSTEM_ZLIB=1")))
(inputs
`(("llvm" ,llvm-julia)
("p7zip" ,p7zip)
;; The bundled version is 3.3.0 so stick to that version. With other
;; versions, we get test failures in 'linalg/arnoldi' as described in
;; <https://bugs.gnu.org/30282>.
("arpack-ng" ,arpack-ng-3.3.0)
("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
("lapack" ,lapack)
("openblas" ,openblas) ;Julia does not build with Atlas
("libunwind" ,libunwind-julia)
("openlibm" ,openlibm)
("mbedtls" ,mbedtls-apache)
("curl" ,curl)
("libgit2" ,libgit2-0.28)
("libssh2" ,libssh2)
("fortran" ,gfortran)
("libuv" ,libuv-julia)
("pcre2" ,pcre2)
("utf8proc" ,utf8proc)
("mpfr" ,mpfr)
("wget" ,wget)
("which" ,which)
("zlib" ,zlib)
("gmp" ,gmp)
("suitesparse" ,suitesparse)
;; Find dependencies versions here:
;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
("objconv"
,(origin
(method url-fetch)
;; No versioned URL, see <https://www.agner.org/optimize/> for updates.
(uri "https://www.agner.org/optimize/objconv.zip")
(file-name "objconv-2018-10-07.zip")
(sha256
(base32
"0wp6ld9vk11f4nnkn56627zmlv9k5vafi99qa3yyn1pgcd61zcfs"))))
("libwhich"
,(let ((commit "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"))
(origin
;; Note: We use a /tarball URL, but that's because Julia's build
;; system checks the hash of that tarball; thus we can't use
;; 'git-fetch'.
(method url-fetch)
(uri (string-append
"https://api.github.com/repos/vtjnash/libwhich/tarball/"
commit))
(file-name (string-append "libwhich-" (string-take commit 7)
".tar.gz"))
(sha256
(base32
"1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
("dsfmt" ,dsfmt)))
(native-inputs
`(("openssl" ,openssl)
("perl" ,perl)
("patchelf" ,patchelf)
("pkg-config" ,pkg-config)
("python" ,python-2)))
(native-search-paths
(list (search-path-specification
(variable "JULIA_LOAD_PATH")
(files (list "share/julia/packages/")))
(search-path-specification
(variable "JULIA_DEPOT_PATH")
(files (list "share/julia/")))))
;; Julia is not officially released for ARM and MIPS.
;; See https://github.com/JuliaLang/julia/issues/10639
(supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
(home-page "https://julialang.org/")
(synopsis "High-performance dynamic language for technical computing")
(description
"Julia is a high-level, high-performance dynamic programming language for
technical computing, with syntax that is familiar to users of other technical
computing environments. It provides a sophisticated compiler, distributed
parallel execution, numerical accuracy, and an extensive mathematical function
library.")
(license license:expat)))