Merge pull request #103783 from doronbehar/pkg/julia/lts

julia_10: rewrite
This commit is contained in:
Michael Raskin 2020-11-17 19:42:16 +00:00 committed by GitHub
commit 8e5f885ba0
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5 changed files with 233 additions and 211 deletions

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@ -1,4 +1,19 @@
import ./shared.nix {
{ stdenv, fetchpatch, fetchurl, fetchzip
# build tools
, gfortran, m4, makeWrapper, patchelf, perl, which, python2
, cmake
# libjulia dependencies
, libunwind, readline, utf8proc, zlib
# standard library dependencies
, curl, fftwSinglePrec, fftw, gmp, libgit2, mpfr, openlibm, openspecfun, pcre2
# linear algebra
, blas, lapack, arpack
# Darwin frameworks
, CoreServices, ApplicationServices
}:
let
majorVersion = "1";
minorVersion = "0";
maintenanceVersion = "4";
@ -6,4 +21,193 @@ import ./shared.nix {
libuvVersion = "ed3700c849289ed01fe04273a7bf865340b2bd7e";
libuvSha256 = "137w666zsjw1p0ma3lf94d75hr1q45sgkfmbizkyji2qm57cnxjs";
dsfmtVersion = "2.2.3";
dsfmt = fetchurl {
url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmtVersion}.tar.gz";
sha256 = "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42";
};
libuv = fetchurl {
url = "https://api.github.com/repos/JuliaLang/libuv/tarball/${libuvVersion}";
sha256 = libuvSha256;
};
rmathVersion = "0.1";
rmath-julia = fetchurl {
url = "https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v${rmathVersion}";
sha256 = "1qyps217175qhid46l8f5i1v8i82slgp23ia63x2hzxwfmx8617p";
};
virtualenvVersion = "15.0.0";
virtualenv = fetchurl {
url = "mirror://pypi/v/virtualenv/virtualenv-${virtualenvVersion}.tar.gz";
sha256 = "06fw4liazpx5vf3am45q2pdiwrv0id7ckv7n6zmpml29x6vkzmkh";
};
libwhichVersion = "81e9723c0273d78493dc8c8ed570f68d9ce7e89e";
libwhich = fetchurl {
url = "https://api.github.com/repos/vtjnash/libwhich/tarball/${libwhichVersion}";
sha256 = "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b";
};
llvmVersion = "6.0.0";
llvm = fetchurl {
url = "http://releases.llvm.org/6.0.0/llvm-${llvmVersion}.src.tar.xz";
sha256 = "0224xvfg6h40y5lrbnb9qaq3grmdc5rg00xq03s1wxjfbf8krx8z";
};
suitesparseVersion = "4.4.5";
suitesparse = fetchurl {
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${suitesparseVersion}.tar.gz";
sha256 = "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43";
};
version = "${majorVersion}.${minorVersion}.${maintenanceVersion}";
in
stdenv.mkDerivation rec {
pname = "julia";
inherit version;
src = fetchzip {
url = "https://github.com/JuliaLang/${pname}/releases/download/v${version}/${pname}-${version}.tar.gz";
sha256 = src_sha256;
};
nativeBuildInputs = [ cmake curl gfortran m4 makeWrapper patchelf perl python2 which ];
# cmake is only used to build the bundled deps
dontUseCmakeConfigure = true;
# We assert that compatible blas and lapack are used.
buildInputs = assert (blas.isILP64 == lapack.isILP64); [
arpack fftw fftwSinglePrec gmp libgit2 libunwind mpfr
pcre2.dev blas lapack openlibm openspecfun readline utf8proc
zlib
]
++ stdenv.lib.optionals stdenv.isDarwin [CoreServices ApplicationServices]
;
patches = [
# Julia recompiles a precompiled file if the mtime stored *in* the
# .ji file differs from the mtime of the .ji file. This
# doesn't work in Nix because Nix changes the mtime of files in
# the Nix store to 1. So patch Julia to accept mtimes of 1.
./allow_nix_mtime.patch
./diagonal-test.patch
./use-system-utf8proc-julia-1.0.patch
];
postPatch = ''
patchShebangs . contrib
for i in backtrace cmdlineargs; do
mv test/$i.jl{,.off}
touch test/$i.jl
done
rm stdlib/Sockets/test/runtests.jl && touch stdlib/Sockets/test/runtests.jl
rm stdlib/Distributed/test/runtests.jl && touch stdlib/Distributed/test/runtests.jl
sed -e 's/Invalid Content-Type:/invalid Content-Type:/g' -i ./stdlib/LibGit2/test/libgit2.jl
sed -e 's/Failed to resolve /failed to resolve /g' -i ./stdlib/LibGit2/test/libgit2.jl
'';
prePatch = ''
mkdir deps/srccache
cp "${dsfmt}" "./deps/srccache/dsfmt-${dsfmtVersion}.tar.gz"
cp "${rmath-julia}" "./deps/srccache/Rmath-julia-${rmathVersion}.tar.gz"
cp "${libuv}" "./deps/srccache/libuv-${libuvVersion}.tar.gz"
cp "${virtualenv}" "./deps/srccache/virtualenv-${virtualenvVersion}.tar.gz"
cp "${libwhich}" "./deps/srccache/libwhich-${libwhichVersion}.tar.gz"
cp "${llvm}" "./deps/srccache/llvm-${llvmVersion}.src.tar.xz"
cp "${suitesparse}" "./deps/srccache/SuiteSparse-${suitesparseVersion}.tar.gz"
'';
makeFlags =
let
arch = stdenv.lib.head (stdenv.lib.splitString "-" stdenv.system);
march = {
x86_64 = stdenv.hostPlatform.platform.gcc.arch or "x86-64";
i686 = "pentium4";
aarch64 = "armv8-a";
}.${arch}
or (throw "unsupported architecture: ${arch}");
# Julia requires Pentium 4 (SSE2) or better
cpuTarget = { x86_64 = "x86-64"; i686 = "pentium4"; aarch64 = "generic"; }.${arch}
or (throw "unsupported architecture: ${arch}");
in [
"ARCH=${arch}"
"MARCH=${march}"
"JULIA_CPU_TARGET=${cpuTarget}"
"PREFIX=$(out)"
"prefix=$(out)"
"SHELL=${stdenv.shell}"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=${if blas.isILP64 then "1" else "0"}"
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_FFTW=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_LIBUNWIND=1"
# We will probably never do that
#"USE_SYSTEM_LLVM=1"
"LLVM_VER=6.0.0"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_OPENSPECFUN=1"
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_PCRE=1"
"PCRE_CONFIG=${pcre2.dev}/bin/pcre2-config"
"PCRE_INCL_PATH=${pcre2.dev}/include/pcre2.h"
"USE_SYSTEM_READLINE=1"
"USE_SYSTEM_UTF8PROC=1"
"USE_SYSTEM_ZLIB=1"
];
LD_LIBRARY_PATH = assert (blas.isILP64 == lapack.isILP64); (stdenv.lib.makeLibraryPath [
arpack fftw fftwSinglePrec gmp libgit2 mpfr blas lapack openlibm
openspecfun pcre2
]);
enableParallelBuilding = true;
doCheck = !stdenv.isDarwin;
checkTarget = "testall";
# Julia's tests require read/write access to $HOME
preCheck = ''
export HOME="$NIX_BUILD_TOP"
'';
preBuild = ''
sed -e '/^install:/s@[^ ]*/doc/[^ ]*@@' -i Makefile
sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
'';
postInstall = ''
# Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
# as using a wrapper with LD_LIBRARY_PATH causes segmentation
# faults when program returns an error:
# $ julia -e 'throw(Error())'
find $(echo $LD_LIBRARY_PATH | sed 's|:| |g') -maxdepth 1 -name '*.${if stdenv.isDarwin then "dylib" else "so"}*' | while read lib; do
if [[ ! -e $out/lib/julia/$(basename $lib) ]]; then
ln -sv $lib $out/lib/julia/$(basename $lib)
fi
done
'';
passthru = {
inherit majorVersion minorVersion maintenanceVersion;
site = "share/julia/site/v${majorVersion}.${minorVersion}";
};
meta = {
description = "High-level performance-oriented dynamical language for technical computing";
homepage = "https://julialang.org/";
license = stdenv.lib.licenses.mit;
maintainers = with stdenv.lib.maintainers; [ raskin rob garrison ];
platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" "aarch64-linux" ];
};
}

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@ -0,0 +1,27 @@
From 9eb180c523b877a53b9e1cf53a4d5e6dad3d7bfe Mon Sep 17 00:00:00 2001
From: Lars Jellema <lars.jellema@gmail.com>
Date: Sat, 19 Sep 2020 13:52:20 +0200
Subject: [PATCH] Use approximate comparisons for diagonal tests
---
stdlib/LinearAlgebra/test/diagonal.jl | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/stdlib/LinearAlgebra/test/diagonal.jl b/stdlib/LinearAlgebra/test/diagonal.jl
index e420d5bc6d..7f1b5d0aec 100644
--- a/stdlib/LinearAlgebra/test/diagonal.jl
+++ b/stdlib/LinearAlgebra/test/diagonal.jl
@@ -450,8 +450,8 @@ end
M = randn(T, 5, 5)
MM = [randn(T, 2, 2) for _ in 1:2, _ in 1:2]
for transform in (identity, adjoint, transpose, Adjoint, Transpose)
- @test lmul!(transform(D), copy(M)) == *(transform(Matrix(D)), M)
- @test rmul!(copy(M), transform(D)) == *(M, transform(Matrix(D)))
+ @test lmul!(transform(D), copy(M)) ≈ *(transform(Matrix(D)), M)
+ @test rmul!(copy(M), transform(D)) ≈ *(M, transform(Matrix(D)))
@test lmul!(transform(DD), copy(MM)) == *(transform(fullDD), MM)
@test rmul!(copy(MM), transform(DD)) == *(MM, transform(fullDD))
end
--
2.28.0

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@ -1,210 +0,0 @@
{ majorVersion
, minorVersion
, maintenanceVersion
, src_sha256
# source deps
, libuvVersion
, libuvSha256
}:
{ stdenv, fetchurl, fetchzip
# build tools
, gfortran, m4, makeWrapper, patchelf, perl, which, python2
, cmake
# libjulia dependencies
, libunwind, readline, utf8proc, zlib
# standard library dependencies
, curl, fftwSinglePrec, fftw, gmp, libgit2, mpfr, openlibm, openspecfun, pcre2
# linear algebra
, blas, lapack, arpack
# Darwin frameworks
, CoreServices, ApplicationServices
}:
with stdenv.lib;
assert (!blas.isILP64) && (!lapack.isILP64);
let
dsfmtVersion = "2.2.3";
dsfmt = fetchurl {
url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmtVersion}.tar.gz";
sha256 = "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42";
};
libuv = fetchurl {
url = "https://api.github.com/repos/JuliaLang/libuv/tarball/${libuvVersion}";
sha256 = libuvSha256;
};
rmathVersion = "0.1";
rmath-julia = fetchurl {
url = "https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v${rmathVersion}";
sha256 = "1qyps217175qhid46l8f5i1v8i82slgp23ia63x2hzxwfmx8617p";
};
virtualenvVersion = "15.0.0";
virtualenv = fetchurl {
url = "mirror://pypi/v/virtualenv/virtualenv-${virtualenvVersion}.tar.gz";
sha256 = "06fw4liazpx5vf3am45q2pdiwrv0id7ckv7n6zmpml29x6vkzmkh";
};
libwhichVersion = "81e9723c0273d78493dc8c8ed570f68d9ce7e89e";
libwhich = fetchurl {
url = "https://api.github.com/repos/vtjnash/libwhich/tarball/${libwhichVersion}";
sha256 = "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b";
};
llvmVersion = "6.0.0";
llvm = fetchurl {
url = "http://releases.llvm.org/6.0.0/llvm-${llvmVersion}.src.tar.xz";
sha256 = "0224xvfg6h40y5lrbnb9qaq3grmdc5rg00xq03s1wxjfbf8krx8z";
};
suitesparseVersion = "4.4.5";
suitesparse = fetchurl {
url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${suitesparseVersion}.tar.gz";
sha256 = "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43";
};
version = "${majorVersion}.${minorVersion}.${maintenanceVersion}";
in
stdenv.mkDerivation rec {
pname = "julia";
inherit version;
src = fetchzip {
url = "https://github.com/JuliaLang/${pname}/releases/download/v${version}/${pname}-${version}.tar.gz";
sha256 = src_sha256;
};
prePatch = ''
export PATH=$PATH:${cmake}/bin
mkdir deps/srccache
cp "${dsfmt}" "./deps/srccache/dsfmt-${dsfmtVersion}.tar.gz"
cp "${rmath-julia}" "./deps/srccache/Rmath-julia-${rmathVersion}.tar.gz"
cp "${libuv}" "./deps/srccache/libuv-${libuvVersion}.tar.gz"
cp "${virtualenv}" "./deps/srccache/virtualenv-${virtualenvVersion}.tar.gz"
cp "${libwhich}" "./deps/srccache/libwhich-${libwhichVersion}.tar.gz"
cp "${llvm}" "./deps/srccache/llvm-${llvmVersion}.src.tar.xz"
cp "${suitesparse}" "./deps/srccache/SuiteSparse-${suitesparseVersion}.tar.gz"
'';
patches = [
./0001.1-use-system-utf8proc.patch
# Julia recompiles a precompiled file if the mtime stored *in* the
# .ji file differs from the mtime of the .ji file. This
# doesn't work in Nix because Nix changes the mtime of files in
# the Nix store to 1. So patch Julia to accept mtimes of 1.
./allow_nix_mtime.patch
];
postPatch = ''
patchShebangs . contrib
for i in backtrace cmdlineargs; do
mv test/$i.jl{,.off}
touch test/$i.jl
done
rm stdlib/Sockets/test/runtests.jl && touch stdlib/Sockets/test/runtests.jl
rm stdlib/Distributed/test/runtests.jl && touch stdlib/Distributed/test/runtests.jl
sed -e 's/Invalid Content-Type:/invalid Content-Type:/g' -i ./stdlib/LibGit2/test/libgit2.jl
sed -e 's/Failed to resolve /failed to resolve /g' -i ./stdlib/LibGit2/test/libgit2.jl
'';
buildInputs = [
arpack fftw fftwSinglePrec gmp libgit2 libunwind mpfr
pcre2.dev blas lapack openlibm openspecfun readline utf8proc
zlib
]
++ stdenv.lib.optionals stdenv.isDarwin [CoreServices ApplicationServices]
;
nativeBuildInputs = [ curl gfortran m4 makeWrapper patchelf perl python2 which ];
makeFlags =
let
arch = head (splitString "-" stdenv.system);
march = { x86_64 = stdenv.hostPlatform.platform.gcc.arch or "x86-64"; i686 = "pentium4"; }.${arch}
or (throw "unsupported architecture: ${arch}");
# Julia requires Pentium 4 (SSE2) or better
cpuTarget = { x86_64 = "x86-64"; i686 = "pentium4"; }.${arch}
or (throw "unsupported architecture: ${arch}");
in [
"ARCH=${arch}"
"MARCH=${march}"
"JULIA_CPU_TARGET=${cpuTarget}"
"PREFIX=$(out)"
"prefix=$(out)"
"SHELL=${stdenv.shell}"
"USE_SYSTEM_BLAS=1"
"USE_BLAS64=${if blas.isILP64 then "1" else "0"}"
"USE_SYSTEM_LAPACK=1"
"USE_SYSTEM_ARPACK=1"
"USE_SYSTEM_FFTW=1"
"USE_SYSTEM_GMP=1"
"USE_SYSTEM_LIBGIT2=1"
"USE_SYSTEM_LIBUNWIND=1"
#"USE_SYSTEM_LLVM=1"
"LLVM_VER=6.0.0"
"USE_SYSTEM_MPFR=1"
"USE_SYSTEM_OPENLIBM=1"
"USE_SYSTEM_OPENSPECFUN=1"
"USE_SYSTEM_PATCHELF=1"
"USE_SYSTEM_PCRE=1"
"PCRE_CONFIG=${pcre2.dev}/bin/pcre2-config"
"PCRE_INCL_PATH=${pcre2.dev}/include/pcre2.h"
"USE_SYSTEM_READLINE=1"
"USE_SYSTEM_UTF8PROC=1"
"USE_SYSTEM_ZLIB=1"
];
LD_LIBRARY_PATH = makeLibraryPath [
arpack fftw fftwSinglePrec gmp libgit2 mpfr blas lapack openlibm
openspecfun pcre2
];
enableParallelBuilding = true;
doCheck = !stdenv.isDarwin;
checkTarget = "testall";
# Julia's tests require read/write access to $HOME
preCheck = ''
export HOME="$NIX_BUILD_TOP"
'';
preBuild = ''
sed -e '/^install:/s@[^ ]*/doc/[^ ]*@@' -i Makefile
sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
'';
postInstall = ''
# Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
# as using a wrapper with LD_LIBRARY_PATH causes segmentation
# faults when program returns an error:
# $ julia -e 'throw(Error())'
find $(echo $LD_LIBRARY_PATH | sed 's|:| |g') -maxdepth 1 -name '*.${if stdenv.isDarwin then "dylib" else "so"}*' | while read lib; do
if [[ ! -e $out/lib/julia/$(basename $lib) ]]; then
ln -sv $lib $out/lib/julia/$(basename $lib)
fi
done
'';
passthru = {
inherit majorVersion minorVersion maintenanceVersion;
site = "share/julia/site/v${majorVersion}.${minorVersion}";
};
meta = {
description = "High-level performance-oriented dynamical language for technical computing";
homepage = "https://julialang.org/";
license = stdenv.lib.licenses.mit;
maintainers = with stdenv.lib.maintainers; [ raskin rob garrison ];
platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
broken = stdenv.isi686;
};
}

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@ -9526,6 +9526,7 @@ in
julia_10 = callPackage ../development/compilers/julia/1.0.nix {
gmp = gmp6;
inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
libgit2 = libgit2_0_27;
};
julia_13 = callPackage ../development/compilers/julia/1.3.nix {