我如何在 mamba 环境中使 IJulia 正常工作？

huangapple
go评论93阅读模式
英文:

How can I get IJulia working inside a mamba environment?

问题

I am having trouble installing IJulia in Julia 1.9.1 inside a mamba environment. The crux of the issue seems to be the compiler not being able to find MbedTLS even though it is installed:

  1. Looking for: ['mbedtls']
  3. conda-forge/noarch                                  13.1MB @   4.4MB/s  3.4s
  4. conda-forge/linux-64                                32.7MB @   4.2MB/s  8.9s
  6. Pinned packages:
  7.   - python 3.11.*
  9. Transaction
  11.   Prefix: /shares/teacher/users/student/mambaforge/envs/jenv
  13.   All requested packages already installed
  1. > Using Pkg
  2. > Pkg.update()
  3. >Pkg.add("IJulia") # this works fine
  4. > Using IJulia # This does not

The error when running the above commands is:

  1. MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d]
  3. Failed to precompile MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d] to "libmbedtls.so".
  4. libmbedx509.so.4: cannot open shared object file: No such file or directory
  5. Stacktrace:
  6.   [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
  7.     @ Base.Libc.Libdl ./libdl.jl:117
  8.   [2] dlopen
  9.     @ ./libdl.jl:116 [inlined]
  10.   [3] dlopen(s::String)
  11.     @ Base.Libc.Libdl ./libdl.jl:116
  12.   [4] __init__()
  13.     @ MbedTLS_jll ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/MbedTLS_jll/src/MbedTLS_jll.jl:42
  14.   [5] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
  15.     @ Base ./loading.jl:1115
  16.   [6] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
  17.     @ Base ./loading.jl:1061
  18.   [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
  19.     @ Base ./loading.jl:1506
  20.   [8] _require(pkg::Base.PkgId, env::String)
  21.     @ Base ./loading.jl:1783
  22.   [9] _require_prelocked(uuidkey::Base.PkgId, env::String)
  23.     @ Base ./loading.jl:1660
  24.  [10] macro expansion
  25.     @ ./loading.jl:1648 [inlined]
  26.  [11] macro expansion
  27.     @ ./lock.jl:267 [inlined]
  28.  [12] require(into::Module, mod::Symbol)
  29.     @ Base ./loading.jl:1611
  30.  [13] include
  31.     @ ./Base.jl:457 [inlined]
  32.  [14] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
  33.     @ Base ./loading.jl:2045
  34.  [15] top-level scope
  35.     @ stdin:3
  36. during initialization of module MbedTLS_jll
  37. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/MbedTLS/lqmet/src/MbedTLS.jl:1
  38. in expression starting at stdin:3
  40. IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a]
  42. Failed to precompile IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a] to "libmbedtls.so".
  43. libmbedx509.so.4: cannot open shared object file: No such file or directory
  44. Stacktrace:
  45.   [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
  46.     @ Base.Libc.Libdl ./libdl.jl:117
  47.   [2] dlopen
  48.     @ ./libdl.jl:116 [inlined]
  49.   [3] dlopen(s::String)
  50.     @ Base.Libc.Libdl ./libdl.jl:116
  51.   [4] __init__()
  52.     @ MbedTLS_jll ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/MbedTLS_jll/src/MbedTLS_jll.jl:42
  53.   [5] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
  54.     @ Base ./loading.jl:1115
  55.   [6] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
  56.     @ Base ./loading.jl:1061
  57.   [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
  58.     @ Base ./loading.jl:1506
  59.   [8] _require(pkg::Base.PkgId, env::String)
  60.     @ Base ./loading.jl:1783
  61.   [9] _require_prelocked(uuidkey::Base.PkgId, env::String)
  62.     @ Base ./loading.jl:1660
  63.  [10] macro expansion
  64.     @ ./loading.jl:1648 [inlined]
  65.  [11] macro expansion
  66.     @ ./lock.jl:267 [inlined]
  67.  [12] require(into::Module, mod::Symbol)
  68.     @ Base ./loading.jl:1611
  69.  [13] include
  70.     @ ./Base.jl:457 [inlined]
  71.  [14] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
  72.     @ Base ./loading.jl:2045
  73.  [15] top-level scope
  74.     @ stdin:3
  75. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/IJulia/Vo51o/src/hmac.jl:1
  76. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/IJulia/Vo51o/src/IJulia.jl:1
  77. in expression starting at stdin:3
  79. Stacktrace:
  80.  [1] pkgerror(msg::String)
  81.    @ Pkg.Types ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/Types.jl:69
  82.  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing
  84. <details>
  85. <summary>英文:</summary>
  87. I am having trouble installing `IJulia` in Julia 1.9.1 inside a mamba environment. The crux of the issue seems to be the compiler not being able to find MbedTLS even though it is installed
  89. ```stdout
  90. Looking for: [&#39;mbedtls&#39;]
  92. conda-forge/noarch                                  13.1MB @   4.4MB/s  3.4s
  93. conda-forge/linux-64                                32.7MB @   4.2MB/s  8.9s
  95. Pinned packages:
  96.   - python 3.11.*
  99. Transaction
  101.   Prefix: /shares/teacher/users/student/mambaforge/envs/jenv
  103.   All requested packages already installed
  1. &gt; Using Pkg
  2. &gt; Pkg.update()
  3. &gt;Pkg.add(&quot;IJulia&quot;) # this works fine
  4. &gt; Using IJulia # This does not

The error when running the above commands is:

  1. MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d]
  3. Failed to precompile MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d] to &quot;/shares/teacher/users/student/mambaforge/envs/jenv/share/julia/compiled/v1.9/MbedTLS/jl_g7s41h&quot;.
  4. ERROR: LoadError: InitError: could not load library &quot;libmbedtls.so&quot;
  5. libmbedx509.so.4: cannot open shared object file: No such file or directory
  6. Stacktrace:
  7.   [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
  8.     @ Base.Libc.Libdl ./libdl.jl:117
  9.   [2] dlopen
  10.     @ ./libdl.jl:116 [inlined]
  11.   [3] dlopen(s::String)
  12.     @ Base.Libc.Libdl ./libdl.jl:116
  13.   [4] __init__()
  14.     @ MbedTLS_jll ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/MbedTLS_jll/src/MbedTLS_jll.jl:42
  15.   [5] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
  16.     @ Base ./loading.jl:1115
  17.   [6] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
  18.     @ Base ./loading.jl:1061
  19.   [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
  20.     @ Base ./loading.jl:1506
  21.   [8] _require(pkg::Base.PkgId, env::String)
  22.     @ Base ./loading.jl:1783
  23.   [9] _require_prelocked(uuidkey::Base.PkgId, env::String)
  24.     @ Base ./loading.jl:1660
  25.  [10] macro expansion
  26.     @ ./loading.jl:1648 [inlined]
  27.  [11] macro expansion
  28.     @ ./lock.jl:267 [inlined]
  29.  [12] require(into::Module, mod::Symbol)
  30.     @ Base ./loading.jl:1611
  31.  [13] include
  32.     @ ./Base.jl:457 [inlined]
  33.  [14] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
  34.     @ Base ./loading.jl:2045
  35.  [15] top-level scope
  36.     @ stdin:3
  37. during initialization of module MbedTLS_jll
  38. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/MbedTLS/lqmet/src/MbedTLS.jl:1
  39. in expression starting at stdin:3
  41. IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a]
  43. Failed to precompile IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a] to &quot;/shares/teacher/users/student/mambaforge/envs/jenv/share/julia/compiled/v1.9/IJulia/jl_sxd2YS&quot;.
  44. ERROR: LoadError: InitError: could not load library &quot;libmbedtls.so&quot;
  45. libmbedx509.so.4: cannot open shared object file: No such file or directory
  46. Stacktrace:
  47.   [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
  48.     @ Base.Libc.Libdl ./libdl.jl:117
  49.   [2] dlopen
  50.     @ ./libdl.jl:116 [inlined]
  51.   [3] dlopen(s::String)
  52.     @ Base.Libc.Libdl ./libdl.jl:116
  53.   [4] __init__()
  54.     @ MbedTLS_jll ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/MbedTLS_jll/src/MbedTLS_jll.jl:42
  55.   [5] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
  56.     @ Base ./loading.jl:1115
  57.   [6] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
  58.     @ Base ./loading.jl:1061
  59.   [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
  60.     @ Base ./loading.jl:1506
  61.   [8] _require(pkg::Base.PkgId, env::String)
  62.     @ Base ./loading.jl:1783
  63.   [9] _require_prelocked(uuidkey::Base.PkgId, env::String)
  64.     @ Base ./loading.jl:1660
  65.  [10] macro expansion
  66.     @ ./loading.jl:1648 [inlined]
  67.  [11] macro expansion
  68.     @ ./lock.jl:267 [inlined]
  69.  [12] require(into::Module, mod::Symbol)
  70.     @ Base ./loading.jl:1611
  71.  [13] include
  72.     @ ./Base.jl:457 [inlined]
  73.  [14] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
  74.     @ Base ./loading.jl:2045
  75.  [15] top-level scope
  76.     @ stdin:3
  77. during initialization of module MbedTLS_jll
  78. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/MbedTLS/lqmet/src/MbedTLS.jl:1
  79. in expression starting at stdin:3
  80. ERROR: LoadError: Failed to precompile MbedTLS [739be429-bea8-5141-9913-cc70e7f3736d] to &quot;/shares/teacher/users/student/mambaforge/envs/jenv/share/julia/compiled/v1.9/MbedTLS/jl_TwrfV9&quot;.
  81. Stacktrace:
  82.   [1] error(s::String)
  83.     @ Base ./error.jl:35
  84.   [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
  85.     @ Base ./loading.jl:2296
  86.   [3] compilecache
  87.     @ ./loading.jl:2163 [inlined]
  88.   [4] _require(pkg::Base.PkgId, env::String)
  89.     @ Base ./loading.jl:1805
  90.   [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
  91.     @ Base ./loading.jl:1660
  92.   [6] macro expansion
  93.     @ ./loading.jl:1648 [inlined]
  94.   [7] macro expansion
  95.     @ ./lock.jl:267 [inlined]
  96.   [8] require(into::Module, mod::Symbol)
  97.     @ Base ./loading.jl:1611
  98.   [9] include(mod::Module, _path::String)
  99.     @ Base ./Base.jl:457
  100.  [10] include(x::String)
  101.     @ IJulia ~/mambaforge/envs/jenv/share/julia/packages/IJulia/Vo51o/src/IJulia.jl:33
  102.  [11] top-level scope
  103.     @ ~/mambaforge/envs/jenv/share/julia/packages/IJulia/Vo51o/src/IJulia.jl:309
  104.  [12] include
  105.     @ ./Base.jl:457 [inlined]
  106.  [13] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
  107.     @ Base ./loading.jl:2045
  108.  [14] top-level scope
  109.     @ stdin:3
  110. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/IJulia/Vo51o/src/hmac.jl:1
  111. in expression starting at /shares/teacher/users/student/mambaforge/envs/jenv/share/julia/packages/IJulia/Vo51o/src/IJulia.jl:1
  112. in expression starting at stdin:3
  114. Stacktrace:
  115.  [1] pkgerror(msg::String)
  116.    @ Pkg.Types ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/Types.jl:69
  117.  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
  118.    @ Pkg.API ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/API.jl:1581
  119.  [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
  120.    @ Pkg.API ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/API.jl:156
  121.  [4] precompile(pkgs::Vector{Pkg.Types.PackageSpec})
  122.    @ Pkg.API ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/API.jl:145
  123.  [5] precompile(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
  124.    @ Pkg.API ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/API.jl:171
  125.  [6] precompile()
  126.    @ Pkg.API ~/mambaforge/envs/jenv/share/julia/stdlib/v1.9/Pkg/src/API.jl:162
  127.  [7] top-level scope
  128.    @ REPL[4]:1

I had a read/write error before this and that I was able debug to the png/svg issue!!! There are some older posts that suggested among other things deleting the logo for julia solves read/write issues. As bizarre as that was, I was able to solve it but this MbedTLS issue does not seem to have a whole lot of discussions behind it. If someone is familiar, could you help me get IJulia working?

答案1

得分: 1

我成功找到了一个折中的解决方法，至少允许IJulia进行预编译。首先，我注意到在conda环境的/lib文件夹中，当安装了mbedtls时，正确的.so文件是存在的。然而，看起来Julia并不会在那里查找。我能够通过将环境变量LD_LIBRARY_PATH设置为这个/lib文件夹的绝对路径来解决这个问题。可以通过创建一个小脚本在激活和取消激活环境时自动完成此操作，参见此答案。

然而，我仍然面临着编译IJulia的另一个问题，即它找不到文件<conda env>/share/julia/cert.pem。我在<conda env>/ssl文件夹中找到了一个cert.pem文件，并将其复制到了share/julia文件夹中。这似乎起作用了，至少IJulia现在可以无问题地预编译。

英文:

I managed to find a hacky workaround to at least allow IJulia to precompile. First I noticed that in the conda environment /lib folder, the correct .so file exists when mbedtls is installed. However, it looks like Julia doesn't look there. I was able to fix this issue by setting the environment variable LD_LIBRARY_PATH to the absolute path of this /lib folder. This can be done automatically upon activate and deactivate of the environment by making a little script, see this answer.

However, I still faced another issue with compiling IJulia, which was that it couldn't find the file &lt;conda env&gt;/share/julia/cert.pem. I found a cert.pem file in the &lt;conda env&gt;/ssl folder and copied this into the share/julia folder. This seemed to work, at least IJulia now precompiles without issue.

huangapple
  • 本文由 发表于 2023年6月29日 21:51:52
  • 转载请务必保留本文链接：https://go.coder-hub.com/76581689.html
  • ijulia-notebook
  • julia
  • mamba
匿名

发表评论

匿名网友

:?: :razz: :sad: :evil: :!: :smile: :oops: :grin: :eek: :shock: :???: :cool: :lol: :mad: :twisted: :roll: :wink: :idea: :arrow: :neutral: :cry: :mrgreen:

确定