diff options
Diffstat (limited to 'gnu/packages/julia.scm')
| -rw-r--r-- | gnu/packages/julia.scm | 246 |
1 files changed, 63 insertions, 183 deletions
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm index fe31e545c9..0bdac66175 100644 --- a/gnu/packages/julia.scm +++ b/gnu/packages/julia.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2020 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -54,26 +55,6 @@ #:use-module (gnu packages wget) #:use-module (ice-9 match)) -(define libuv-julia - (let ((commit "fb3e3364c33ae48c827f6b103e05c3f0e78b79a9") - (revision "3")) - ;; When upgrading Julia, also upgrade this. Get the commit from - ;; https://github.com/JuliaLang/julia/blob/v1.6.1/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") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1kqpn19d20aka30h6q5h8lnzyp0vw0xzgx0wm4w2r5j6yf76m2hr")))) - (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 @@ -90,144 +71,30 @@ (base32 "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3")) (patches - (list - (julia-patch "libunwind-prefer-extbl" - "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1") - (julia-patch "libunwind-static-arm" - "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") - (julia-patch "libunwind-cfa-rsp" - "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z"))))) + (append + ;; Fix linker issue for i686-linux because GCC10 changed default + ;; (see '-fno-common' option). + (search-patches "libunwind-julia-fix-GCC10-fno-common.patch") + (list + (julia-patch "libunwind-prefer-extbl" + "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1") + (julia-patch "libunwind-static-arm" + "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq") + (julia-patch "libunwind-cfa-rsp" + "1aswjhvysahhldbzh1afbf0hsjxrvs6xidsz2i7s1cjkjbdiia1z")))))) (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 ".patch")) -(define (julia-patch name sha) +(define-public (julia-patch name sha) (let ((version "1.6.1")) (origin (method url-fetch) (uri (julia-patch-url version name)) (sha256 (base32 sha)) (file-name name)))) -(define llvm-julia - (package - (inherit llvm-11) - (name "llvm-julia") - (source (origin - (inherit (package-source llvm-11)) - ;; 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-D27629-AArch64-large_model_6.0.1" - "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z") - '("llvm8-D34078-vectorize-fdiv" - "19spqc3xsazn1xs9gpcgv9ldadfkv49rmc5khl7sf1dlmhgi4602") - '("llvm-7.0-D44650" - "1h55kkmkiisfj6sk956if2bcj9s0v6n5czn8dxb870vp5nccj3ir") - '("llvm-6.0-DISABLE_ABI_CHECKS" - "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg") - '("llvm9-D50010-VNCoercion-ni" - "1s1d3sjsiq4vxg7ncy5cz56zgy5vcq6ls3iqaiqkvr23wyryqmdx") - '("llvm7-revert-D44485" - "0f59kq3p3mpwsbmskypbi4zn01l6ig0x7v2rjp08k2r8z8m6fa8n") - '("llvm-11-D75072-SCEV-add-type" - "176xi1lnbnv2rcs05ywhyb7pd0xgmibayvwzksksg44wg2dh8mbx") - '("llvm-julia-tsan-custom-as" - "0awh40kf6lm4wn1nsjd1bmhfwq7rqj811szanp2xkpspykw9hg9s") - '("llvm-D80101" - "1gsdwmgmpbignvqyxcnlprj899259p3dvdznlncd84ss445qgq3j") - '("llvm-D84031" - "0nks9sbk7p0r5gyr0idrmm93a5fmdai8kihz9532dx4zhcvvqbjc") - '("llvm-10-D85553" - "1zjq7j9q2qp56hwkc8yc8f0z7kvam3j7hj8sb7qyd77r255ff78l") - '("llvm-10-unique_function_clang-sa" - "1jys9w2zqk3dasnxqh0qz5ij7rxi6mkgq9pqjsclmamr5169zyan") - ;'("llvm-D88630-clang-cmake" - ; "0rs6s71nqnjkny7i69gqazhqj5jqfdr0bkxs2v5a55sfx8fa1k54") - '("llvm-11-D85313-debuginfo-empty-arange" - "1f672d5385xpgb8yrim8d3b7wg2z1l81agnshm1q61kdvjixqx32") - '("llvm-11-D90722-rtdyld-absolute-relocs" - "0kmnai229yyxkmpk9lxd180mcnhk2i8d87k2sg89gc8as18w10r6") - '("llvm-invalid-addrspacecast-sink" - "1n1b7j4s80vj7x5377aj9vyphmxx1q6bm0chhkxp6zsy3mx3g2ry") - '("llvm-11-D92906-ppc-setjmp" - "0cmd4dsblp7a8m03j16dqxws0ijh55zf4jzzxmj341qxa1gamdp9") - '("llvm-11-PR48458-X86ISelDAGToDAG" - "0vwzvlhsdazhxg4gj8g2f00a4f8qc5cgac23w575xk3pgba1jh6y") - '("llvm-11-D93092-ppc-knownbits" - "1748bypsc7c9lbs3fnkv0kwvch6bn85kj98j4jdaz254ig0wa6xj") - '("llvm-11-D93154-globalisel-as" - "1k5wd4z3pa7zj0gyjkif7viqj906dhqlbb7dc95gig40nbxv6zpj") - '("llvm-11-ppc-half-ctr" - "0piywisfz6cmw3133kz7vzhiqflq2y7igakqxlym0gi8pqylv7w9") - '("llvm-11-ppc-sp-from-bp" - "1wmg3485cx5f9pbykyl3jibk1wwv4w1x30hl4jyfndzr2yh8azf9") - '("llvm-rGb498303066a6-gcc11-header-fix" - "0hkd4rwhvh8g2yh13g29wiwnjpv2yd1hdyiv1ryw8izl25bz9c67") - '("llvm-11-D94813-mergeicmps" - "0cmy0ywkgyrdcvr9bd6pd912lyd4gcsrib4z0v05dwgcdxhk7y29") - '("llvm-11-D94980-CTR-half" - "1yf8cxib3z8hz7zi9n6v2g2c6vpfr4slq9hpx8m8yq8f1jbyw3fw") - '("llvm-11-D94058-sext-atomic-ops" - "1x6p6k6q651z5jcqxx8vj17cxnv196mka7mwn7dpp6c23lwgfdpb") - '("llvm-11-D96283-dagcombine-half" - "0lv4iq2f8qrcz1xyxfic3bcr5p0aqam3a7c6pp6fnw3riixm096k")))) - (patch-flags '("-p1")))) - (arguments - (substitute-keyword-arguments (package-arguments llvm-11) - ((#:phases phases) - `(modify-phases ,phases - (add-after 'unpack 'patch-round-two - ;; We have to do the patching in two rounds because we can't - ;; pass '-p1' and '-p2' in the source field. - (lambda* (#:key inputs #:allow-other-keys) - (map (lambda (patchname) - (invoke "patch" patchname "-p2")) - (list "llvm-11-AArch64-FastIsel-bug" - "llvm-11-D97435-AArch64-movaddrreg" - "llvm-11-D97571-AArch64-loh" - "llvm-11-aarch64-addrspace")))))) - ((#:build-type _) "Release") - ((#:configure-flags flags) - `(list - ;; 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")))) - (inputs - (append - (package-inputs llvm-11) - `(("llvm-11-AArch64-FastIsel-bug" - ,(julia-patch "llvm-11-AArch64-FastIsel-bug" - "1m2vddj1mw4kbij8hbrx82piyy6bvr2x7wwdnlxfaqcm72ipzyh9")) - ("llvm-11-D97435-AArch64-movaddrreg" - ,(julia-patch "llvm-11-D97435-AArch64-movaddrreg" - "10jnavq9ljkj7j2gqj2zd1pwqpqb5zs3zp9h96pmz0djbmxwa86y")) - ("llvm-11-D97571-AArch64-loh" - ,(julia-patch "llvm-11-D97571-AArch64-loh" - "128zcbg1w1j7hngsf7z1a7alc6lig6l2rqgjp6i8nk3k3f842v6n")) - ("llvm-11-aarch64-addrspace" - ,(julia-patch "llvm-11-aarch64-addrspace" - "0ckbzgfirxrf2d5bpinpngp7gnilbjrk0cbdfyl3h6f5v6i6xj6m"))))))) - (define-public libwhich (package (name "libwhich") @@ -261,7 +128,7 @@ #t))))) (native-inputs ;; used for tests - `(("zlib" ,zlib))) + (list zlib)) (build-system gnu-build-system) (home-page "https://github.com/vtjnash/libwhich") (synopsis "Like @code{which}, for dynamic libraries") @@ -272,7 +139,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (define-public julia (package (name "julia") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (string-append @@ -280,9 +147,10 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") version "/julia-" version ".tar.gz")) (sha256 (base32 - "0plbj4laifzz8ppk889iv3gaxj1mdddzv7yad6ghml6bfnn24r6m")) + "1515x8fs25l3f9csbmd1v4nm041zvjnvigy6s5iidy4yrkwdx4r5")) (patches - (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch")))) + (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch" + "julia-allow-parallel-build.patch")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -328,8 +196,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (("(install: .*) \\$\\(BUILDROOT\\)/doc/_build/html/en/index.html" _ line) (string-append line "\n")) (("src ui doc deps") - "src ui deps")) - #t)) + "src ui deps")))) (add-after 'unpack 'use-system-libwhich (lambda* (#:key inputs #:allow-other-keys) ;; don't build it @@ -338,15 +205,13 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ;; call our version (substitute* "base/Makefile" (("\\$\\$\\(build_depsbindir\\)/libwhich") - (string-append (assoc-ref inputs "libwhich") "/bin/libwhich"))) - #t)) + (search-input-file inputs "/bin/libwhich"))))) (add-after 'unpack 'change-number-of-precompile-statements (lambda _ ;; Remove nss-certs drops the number of statements below 1200, ;; causing the build to fail prematurely. (substitute* "contrib/generate_precompile.jl" - (("1200") "1100")) - #t)) + (("1200") "1100")))) ;; For some reason libquadmath is unavailable on this architecture. ;; https://github.com/JuliaLang/julia/issues/41613 ,@(if (target-aarch64?) @@ -384,14 +249,11 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* "base/Makefile" (("\\$\\(build_includedir\\)/uv/errno.h") - (string-append (assoc-ref inputs "libuv") - "/include/uv/errno.h"))) - #t)) + (search-input-file inputs "/include/uv/errno.h"))))) (add-before 'build 'replace-default-shell (lambda _ (substitute* "base/client.jl" - (("/bin/sh") (which "sh"))) - #t)) + (("/bin/sh") (which "sh"))))) (add-before 'build 'shared-objects-paths (lambda* (#:key inputs #:allow-other-keys) (let ((jlpath @@ -455,26 +317,37 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (to "suitesparse" "libsuitesparseconfig")) (((from "libumfpack")) (to "suitesparse" "libumfpack"))) (substitute* (jlpath "Zlib") - (((from "libz")) (to "zlib" "libz")))) - #t)) + (((from "libz")) (to "zlib" "libz")))))) + (add-after 'unpack 'enable-parallel-tests + (lambda* (#:key parallel-tests? #:allow-other-keys) + (setenv "JULIA_CPU_THREADS" (if parallel-tests? + (number->string (parallel-job-count)) + "1")) + (format #t "JULIA_CPU_THREADS environment variable set to ~a~%" + (getenv "JULIA_CPU_THREADS")))) (add-after 'unpack 'adjust-test-suite (lambda* (#:key inputs #:allow-other-keys) - (let (;(pcre2 (assoc-ref inputs "pcre2")) + (let ((pcre2 (assoc-ref inputs "pcre2")) (mbedtls-apache (assoc-ref inputs "mbedtls")) (mpfr (assoc-ref inputs "mpfr")) + (gmp (assoc-ref inputs "gmp")) + (nghttp2 (assoc-ref inputs "libnghttp2")) (suitesparse (assoc-ref inputs "suitesparse"))) ;; Some tests only check to see if the input is the correct version. - ;(substitute* "stdlib/PCRE2_jll/test/runtests.jl" - ; (("10.36.0") ,(package-version pcre2))) + (substitute* "stdlib/PCRE2_jll/test/runtests.jl" + (("10.36.0") ,(package-version pcre2))) (substitute* "stdlib/MbedTLS_jll/test/runtests.jl" (("2.24.0") ,(package-version mbedtls-apache))) (substitute* "stdlib/MPFR_jll/test/runtests.jl" (("4.1.0") ,(package-version mpfr))) + (substitute* "stdlib/GMP_jll/test/runtests.jl" + (("6.2.0") ,(package-version gmp))) + (substitute* "stdlib/nghttp2_jll/test/runtests.jl" + (("1.41.0") ,(package-version nghttp2))) (substitute* "stdlib/SuiteSparse_jll/test/runtests.jl" (("5004") ,(string-replace-substring (version-major+minor - (package-version suitesparse)) "." "0"))) - #t))) + (package-version suitesparse)) "." "0")))))) (add-before 'check 'disable-broken-tests (lambda _ ;; disabling REPL tests because they require a stdin @@ -487,8 +360,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ;; Dates/io tests fail on master when networking is unavailable ;; https://github.com/JuliaLang/julia/issues/34655 (substitute* "stdlib/Dates/test/io.jl" - (("\"Dates.Date") "\"Date") - (("\"Dates.Time") "\"Time")) + (("using Dates") "import Dates +using Dates: @dateformat_str, Date, DateTime, DateFormat, Time")) ;; Upstream bug I found when packaging ;; https://github.com/JuliaLang/julia/issues/35785 (substitute* "test/file.jl" @@ -512,7 +385,19 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (substitute* "test/cmdlineargs.jl" (("test v\\[3") "test_broken v[3") (("test isempty\\(v\\[3") "test_broken isempty(v[3")) - #t)) + ;; These tests randomly fails because they depend on CPU. + (substitute* "stdlib/LinearAlgebra/test/matmul.jl" + ;; Fixed in v1.6.4 (see: + ;; https://github.com/JuliaLang/julia/blob/v1.6.4/ + ;; stdlib/LinearAlgebra/test/matmul.jl#L155). + (("@test mul\\!\\(C, vf, transpose\\(vf\\), 2, 3\\)\ + == 2vf\\*vf' \\.\\+ 3C0") + "@test mul!(C, vf, transpose(vf), 2, 3) ≈ 2vf*vf' .+ 3C0")) + (substitute* "test/math.jl" + ;; @test_broken cannot be used because if the test randomly + ;; passes, then it also raises an error. + (("@test isinf\\(log1p\\(-one\\(T\\)\\)\\)") + " ")))) (add-before 'install 'symlink-libraries (lambda* (#:key inputs outputs #:allow-other-keys) (let ((link @@ -533,8 +418,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (link "zlib" "usr/lib/julia/" "libz\\.so") (link "libunwind" "usr/lib/julia/" "libunwind\\.so") (symlink (string-append (assoc-ref inputs "p7zip") "/bin/7z") - "usr/libexec/7z") - #t))) + "usr/libexec/7z")))) (add-after 'install 'symlink-llvm-utf8proc (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -548,9 +432,8 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (basename file))))) (find-files (string-append (assoc-ref inputs pkgname) "/lib") pred))))) - (link "llvm" "libLLVM-11\\.so") - (link "utf8proc" "libutf8proc\\.so") - #t))) + (link "llvm" "libLLVM-11jl\\.so") + (link "utf8proc" "libutf8proc\\.so")))) (add-after 'install 'make-wrapper (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -561,8 +444,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") `("JULIA_LOAD_PATH" ":" prefix ("" "$JULIA_LOAD_PATH")) `("JULIA_DEPOT_PATH" ":" prefix - ("" "$JULIA_DEPOT_PATH")))) - #t)))) + ("" "$JULIA_DEPOT_PATH")))))))) #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")) @@ -638,7 +520,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ("gfortran:lib" ,gfortran "lib") ("gmp" ,gmp) ("lapack" ,lapack) - ("libgit2" ,libgit2) + ("libgit2" ,libgit2-1.1) ("libnghttp2" ,nghttp2 "lib") ("libssh2" ,libssh2) ("libunwind" ,libunwind-julia) @@ -649,9 +531,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") ("openblas" ,openblas) ("openlibm" ,openlibm) ("p7zip" ,p7zip) - ;; pcre2-10.35 has a bug with the JIT regex parser: - ;; https://github.com/JuliaLang/julia/issues/40231#issuecomment-812753324 - ("pcre2" ,pcre2-10.36) + ("pcre2" ,pcre2) ("suitesparse" ,suitesparse) ("utf8proc" ,utf8proc-2.6.1) ("wget" ,wget) @@ -670,7 +550,7 @@ libraries. It is also a bit like @code{ldd} and @code{otool -L}.") (native-search-paths (list (search-path-specification (variable "JULIA_LOAD_PATH") - (files (list "share/julia/packages/"))) + (files (list "share/julia/loadpath/"))) (search-path-specification (variable "JULIA_DEPOT_PATH") (files (list "share/julia/"))))) |