Closed unsoundsystem closed 4 years ago
KristofferC
commented
4 years ago This looks the same as https://discourse.julialang.org/t/pkg-crashes/34750/3.
Solution is to use the official binaries at https://julialang.org/downloads/. Please comment if this doesn't fix the problem.
unsoundsystem
commented
4 years ago Fixed thank you very much!!!
alyst
commented
4 years ago Using an official binary could be a solution, but I'm using Julia built with MKL, so I need a way to compile it with the recent versions of the OS packages. There's a corresponding ArchLinux Issue #65540. Eventually, it would be nice to fix it in the official package. For me it looks like http-parser-2.9.3 requires a newer version of libgit2. Which, in turn, requires an update to stdlib/LibGit2. Maybe some of the Julia devs can provide more details on the issue, so that the efforts in #65540 would be more efficient?
KristofferC
commented
4 years ago MKL.jl should work with the official binaries.
alyst
commented
4 years ago Thanks for the suggestion, I was not aware of MKL.jl! Now I'm trying to use julia-bin AUR package, which provides the official 1.3.1 binaries. However, using MKL.jl "as is" is a no-go for me, as it needs to update /usr/.../julia/base/sysimg.jl managed by the OS package manager. I'm now trying to use https://github.com/tkf/JuliaManager.jl to have a system image in my home folder, but this package is not up-to-date and conflicts with MKL.jl (because of PackageCompiler.jl). I can try fixing it myself (but I see that it's already more than just fixing Project.toml), unless there's better solution.
KristofferC
commented
4 years ago I meant just downloading and using the official binaries without a package manager. It might be possible for PackageCompiler to not require write access to that folder though.
alyst
commented
4 years ago I think I understand how supporting rolling release Linux distributions looks from the Julia developer perspective, but I would really like to avoid manually maintaining multiple software packages for multiple users in their home folders.
I'm trying now to automate the process of building MKL-enabled system image.
Here's an excerpt from the modified julia-bin AUR (${srcdir}/julia-${pkgver} is where the official binaries are extracted):
build() {
# rebuild sysimage with MKL support
rm -rf julia-${pkgver}/tmpdepot
mkdir -p julia-${pkgver}/tmpdepot/tmpenv
cd julia-${pkgver}/tmpdepot/tmpenv
JULIA_DEPOT_PATH=${srcdir}/julia-${pkgver}/tmpdepot ${srcdir}/julia-${pkgver}/bin/julia \
-H ${srcdir}/julia-${pkgver}/bin \
--startup-file=no \
--project=. \
${srcdir}/build_sysimg_with_mkl.jl
}and here's build_sysimg_with_mkl.jl that gets called:
using Pkg
Pkg.add(PackageSpec(url="https://github.com/JuliaComputing/MKL.jl"))However, I'm getting this error:
...
Building MKL → `~/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/MKL/1edTo/deps/build.log`
┌ Error: Error building `MKL`:
│ error during bootstrap:
│ LoadError("/tmp/jl_8dlP7m/sysimage_packagecompiler_4630637a-614a-11ea-16df-07de228ef25d.jl", 16, ArgumentError("Package MKL not found in current path:\n- Run `import Pkg; Pkg.add(\"MKL\")` to install the MKL package.\n"))
│ rec_backtrace at /buildworker/worker/package_linux64/build/src/stackwalk.c:94
│ record_backtrace at /buildworker/worker/package_linux64/build/src/task.c:224 [inlined]
│ jl_throw at /buildworker/worker/package_linux64/build/src/task.c:461
│ require at ./loading.jl:887
.... <skip until the end of the log>
│ [ Info: Splicing in code to load MKL in /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/bin/../share/julia/base/sysimg.jl
│ [ Info: getting precompile script from: https://raw.githubusercontent.com/JuliaLang/julia/release-1.3/contrib/generate_precompile.jl
│ [ Info: PackageCompiler: creating base system image (incremental=false)...
│ ERROR: LoadError: failed process: Process(`/home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/bin/julia --color=yes --startup-file=no --cpu-target native --sysimage=/tmp/jl_8dlP7m/corecompiler.ji -g1 -O0 --output-ji=/tmp/jl_8dlP7m/sys.ji /tmp/jl_8dlP7m/sysimage_packagecompiler_4630637a-614a-11ea-16df-07de228ef25d.jl`, ProcessExited(1)) [1]
│
│ Stacktrace:
│ [1] pipeline_error at ./process.jl:525 [inlined]
│ [2] read(::Cmd) at ./process.jl:412
│ [3] (::PackageCompiler.var"#2#3"{String,Array{String,1},String,String,String,String})() at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/PackageCompiler/D8oaG/src/PackageCompiler.jl:157
│ [4] cd(::PackageCompiler.var"#2#3"{String,Array{String,1},String,String,String,String}, ::String) at ./file.jl:104
│ [5] #create_fresh_base_sysimage#1(::String, ::typeof(PackageCompiler.create_fresh_base_sysimage), ::Array{String,1}) at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/PackageCompiler/D8oaG/src/PackageCompiler.jl:141
│ [6] #create_fresh_base_sysimage at ./tuple.jl:0 [inlined]
│ [7] #create_sysimage#5(::Nothing, ::String, ::Array{String,1}, ::Array{String,1}, ::Bool, ::Bool, ::Bool, ::String, ::String, ::Nothing, ::Bool, ::typeof(create_sysimage), ::Array{Symbol,1}) at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/PackageCompiler/D8oaG/src/PackageCompiler.jl:414
│ [8] (::PackageCompiler.var"#kw##create_sysimage")(::NamedTuple{(:incremental, :replace_default, :script),Tuple{Bool,Bool,String}}, ::typeof(create_sysimage), ::Array{Symbol,1}) at ./none:0 (repeats 2 times)
│ [9] top-level scope at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/MKL/1edTo/src/install.jl:107
│ [10] eval at ./boot.jl:330 [inlined]
│ [11] change_blas_library(::String) at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/MKL/1edTo/src/install.jl:105
│ [12] enable_mkl_startup() at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/MKL/1edTo/src/install.jl:82
│ [13] top-level scope at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/MKL/1edTo/deps/build.jl:5
│ [14] include at ./boot.jl:328 [inlined]
│ [15] include_relative(::Module, ::String) at ./loading.jl:1105
│ [16] include(::Module, ::String) at ./Base.jl:31
│ [17] include(::String) at ./client.jl:424
│ [18] top-level scope at none:5
│ in expression starting at /home/theuser/aur/julia-mkl-bin/src/julia-1.3.1/tmpdepot/packages/MKL/1edTo/deps/build.jl:5
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649Do I miss something very simple?
Segfault occur when updating julia packages. The problem happen after update of archlinux.
error message