Julia + Centos - 无法构建 Arpack

Question

我使用 yum 和 epel 在我的 CentOS 机器上按照 [平台特定说明 (https://julialang.org/downloads/platform.html) 中的说明安装了 julia (v1.1.1)。

Julia 工作正常，但是在预编译包时（例如using DataFrames），我得到了

[ Info: Precompiling GLM [38e38edf-8417-5370-95a0-9cbb8c7f171a]
ERROR: LoadError: No deps.jl file could be found. Please try running Pkg.build("Arpack").
Currently, the build command might fail when Julia has been built from source
and the recommendation is to use the official binaries from julialang.org.
For more info see https://github.com/JuliaLinearAlgebra/Arpack.jl/issues/5.

我对编译、从源代码构建等方面了解不足，无法解决这个问题。我想如果我只是从主页下载 Julia 并在该文件夹中使用它，它会工作得很好。但我更喜欢通过包管理器使用它来自动接收更新。

我该如何解决这个问题？

Answer 1

不幸的是，这是意料之中的，因为 Arpack.jl 期望 OpenBLAS 被称为 libopenblas64_.so.0，而在 Fedora/CentOS 中它是 libopenblasp64_.so.0。您可以使用sudo ln -s /lib64/libopenblas64p_.so.0 ~/.julia/packages/Arpack/*/deps/lib/libopenblas64_.so.0 解决此问题。我将尝试与 Arpack.jl 开发人员一起寻找解决方案。

Answer 2

所以我最终通过原始 julialang 页面的帮助解决了这个问题。出于某种原因，如果您通过# yum install julia（启用了 epel）安装 julia，则无法构建Arpack。 Pkg.build("Arpack") 失败。

如果您从官方页面下载 julia 并将其添加到路径中，它仍然会抛出相同的错误消息。但是，如果您启动 julia 并事先运行 Pkg.build("Arpack")，它就可以正常工作！

Answer 3

我确认@MilanBouchet-Valat 解决方案有效。以下是 Debian 发行版的一些细节。

我已经使用 Debian 4.19.37-5 包管理器（例如 synaptic）安装了 Julia。我有

julia> versioninfo()

打印

Julia Version 1.0.4
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: Intel(R) Xeon(R) CPU E5-2603 v3 @ 1.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, haswell)

• 症状

在 Julia 下，我在尝试安装 Arpack 包时遇到了“预期”错误：

(v1.0) pkg> add Arpack

打印

 Resolving package versions...
  Updating `~/.julia/environments/v1.0/Project.toml`
  [7d9fca2a] + Arpack v0.3.1
  Updating `~/.julia/environments/v1.0/Manifest.toml`
 [no changes]

然后

julia> using Arpack

打印

[ Info: Precompiling Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97]
ERROR: LoadError: No deps.jl file could be found. Please try running 
Pkg.build("Arpack").

Currently, the build command might fail when Julia has been built from source
and the recommendation is to use the official binaries from julialang.org.
For more info see https://github.com/JuliaLinearAlgebra/Arpack.jl/issues/5.

Stacktrace:
 [1] top-level scope at /home/picaud/.julia/packages/Arpack/cu5By/src/Arpack.jl:19
 [2] include at ./boot.jl:317 [inlined]
 [3] include_relative(::Module, ::String) at ./loading.jl:1044
 [4] include(::Module, ::String) at ./sysimg.jl:29
 [5] top-level scope at none:2
 [6] eval at ./boot.jl:319 [inlined]
 [7] eval(::Expr) at ./client.jl:393
 [8] top-level scope at ./none:3
in expression starting at /home/picaud/.julia/packages/Arpack/cu5By/src/Arpack.jl:16
ERROR: Failed to precompile Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97] to /home/picaud/.julia/compiled/v1.0/Arpack/X5VZL.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1203
 [3] _require(::Base.PkgId) at ./loading.jl:960
 [4] require(::Base.PkgId) at ./loading.jl:858
 [5] require(::Module, ::Symbol) at ./loading.jl:853

然而

 pkg> build Arpack

打印

  Building Arpack → `~/.julia/packages/Arpack/cu5By/deps/build.log`
┌ Error: Error building `Arpack`: 
│ ERROR: LoadError: LibraryProduct(nothing, ["libarpack"], :libarpack, "Prefix(/home/picaud/.julia/packages/Arpack/cu5By/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] #write_deps_file#152(::Bool, ::Function, ::String, ::Array{LibraryProduct,1}) at /home/picaud/.julia/packages/BinaryProvider/TcAwt/src/Products.jl:414
│  [3] (::getfield(BinaryProvider, Symbol("#kw##write_deps_file")))(::NamedTuple{(:verbose,),Tuple{Bool}}, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at ./none:0
│  [4] top-level scope at none:0
│  [5] include at ./boot.jl:317 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1044
│  [7] include(::Module, ::String) at ./sysimg.jl:29
│  [8] include(::String) at ./client.jl:392
│  [9] top-level scope at none:0
│ in expression starting at /home/picaud/.julia/packages/Arpack/cu5By/deps/build.jl:74
└ @ Pkg.Operations /build/julia-gbfU8y/julia-1.0.4+dfsg/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1096

• 诊断

您可以检查这是否是一个依赖问题：

ldd ~/.julia/packages/Arpack/cu5By/deps/usr/lib/libarpack.so

打印

    linux-vdso.so.1 (0x00007ffc179a1000)
    libopenblas64_.so.0 => not found            <----
    libgfortran.so.5 => /usr/lib/x86_64-linux-gnu/libgfortran.so.5 (0x00007feea073d000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007feea05ba000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007feea05a0000)
    libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007feea0557000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007feea0396000)
    /lib64/ld-linux-x86-64.so.2 (0x00007feea0c67000)

Debian 发行版：

find /usr/lib/ -name libopenblas\*

打印

/usr/lib/x86_64-linux-gnu/libopenblas.so
/usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.6.a
/usr/lib/x86_64-linux-gnu/libopenblas64_.so.0
/usr/lib/x86_64-linux-gnu/julia/libopenblas.so
/usr/lib/x86_64-linux-gnu/libopenblas.so.0
/usr/lib/x86_64-linux-gnu/libopenblas.a
/usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.6.so

• “修复”

用root权限（su）创建符号链接

ln -s /usr/lib/x86_64-linux-gnu/libopenblas.so /usr/lib/x86_64-linux-gnu/libopenblas64_.so.0

现在可以了

pkg> build Arpack
Building Arpack → `~/.julia/packages/Arpack/cu5By/deps/build.log`

然后

using Arpack
[ Info: Precompiling Arpack [7d9fca2a-8960-54d3-9f78-7d1dccf2cb97]

没问题