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Hard-to-debug Julia error message in container #13

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Robinlovelace opened this issue Sep 22, 2024 · 4 comments
Open

Hard-to-debug Julia error message in container #13

Robinlovelace opened this issue Sep 22, 2024 · 4 comments

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@Robinlovelace
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Julia seems to work in the latest version of this repo running in Devcontainer.

However, when you try to build the website with quarto preview it fails:

6/11 [unnamed-chunk-3]
Julia version 1.10.5 at location /opt/julia/bin will be used.
Loading setup script for JuliaCall...
┌ Error: Error during initialization of module CHOLMOD
│   exception =
│    could not load symbol "SuiteSparse_config_malloc_func_set":
│    /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.5: undefined symbol: SuiteSparse_config_malloc_func_set
│    Stacktrace:
│      [1] __init__()
│        @ SparseArrays.CHOLMOD /opt/julia/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:224
│      [2] run_module_init(mod::Module, i::Int64)
│        @ Base ./loading.jl:1134
│      [3] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
│        @ Base ./loading.jl:1122
│      [4] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
│        @ Base ./loading.jl:1067
│      [5] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
│        @ Base ./loading.jl:1481
│      [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
│        @ Base ./loading.jl:1574
│      [7] _require(pkg::Base.PkgId, env::String)
│        @ Base ./loading.jl:1938
│      [8] __require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1812
│      [9] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│     [10] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│     [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1803
│     [12] macro expansion
│        @ ./loading.jl:1790 [inlined]
│     [13] macro expansion
│        @ ./lock.jl:267 [inlined]
│     [14] __require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1753
│     [15] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│     [16] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│     [17] require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1746
│     [18] top-level scope
│        @ /usr/local/lib/R/site-library/JuliaCall/julia/setup.jl:13
│     [19] include(mod::Module, _path::String)
│        @ Base ./Base.jl:495
│     [20] top-level scope
│        @ none:1
└ @ SparseArrays.CHOLMOD /opt/julia/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:241
┌ Error: Error during initialization of module CHOLMOD
│   exception =
│    could not load symbol "SuiteSparse_config_malloc_func_set":
│    /usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so.5: undefined symbol: SuiteSparse_config_malloc_func_set
│    Stacktrace:
│      [1] __init__()
│        @ SparseArrays.CHOLMOD /opt/julia/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:224
│      [2] run_module_init(mod::Module, i::Int64)
│        @ Base ./loading.jl:1134
│      [3] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
│        @ Base ./loading.jl:1122
│      [4] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
│        @ Base ./loading.jl:1067
│      [5] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
│        @ Base ./loading.jl:1481
│      [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
│        @ Base ./loading.jl:1574
│      [7] _require(pkg::Base.PkgId, env::String)
│        @ Base ./loading.jl:1938
│      [8] __require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1812
│      [9] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│     [10] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│     [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1803
│     [12] macro expansion
│        @ ./loading.jl:1790 [inlined]
│     [13] macro expansion
│        @ ./lock.jl:267 [inlined]
│     [14] __require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1753
│     [15] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│     [16] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│     [17] require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1746
│     [18] include
│        @ ./Base.jl:495 [inlined]
│     [19] 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)
│        @ Base ./loading.jl:2222
│     [20] top-level scope
│        @ stdin:3
│     [21] eval
│        @ ./boot.jl:385 [inlined]
│     [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│        @ Base ./loading.jl:2076
│     [23] include_string
│        @ ./loading.jl:2086 [inlined]
│     [24] exec_options(opts::Base.JLOptions)
│        @ Base ./client.jl:316
│     [25] _start()
│        @ Base ./client.jl:552
└ @ SparseArrays.CHOLMOD /opt/julia/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:241
Finish loading setup script for JuliaCall.
  Activating project at `/workspaces/cross_language_projects`
Error:
! Error happens in Julia.
InitError: could not load library "/root/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib/libhdf5.so"
/usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_4' not found (required by /root/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib/libhdf5.so)
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:116
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/inPJn/src/products/library_generators.jl:63 [inlined]
  [4] __init__()
    @ HDF5_jll ~/.julia/packages/HDF5_jll/3C0GU/src/wrappers/x86_64-linux-gnu-libgfortran5-cxx11-mpi+mpich.jl:15
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1134
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1122
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1067
  [8] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
    @ Base ./loading.jl:1481
  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
    @ Base ./loading.jl:1574
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1938
 [11] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
 [12] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [13] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [14] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
 [15] macro expansion
    @ ./loading.jl:1790 [inlined]
 [16] macro expansion
    @ ./lock.jl:267 [inlined]
 [17] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
 [18] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
 [19] invoke_in_world
    @ ./essentials.jl:923 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
 [21] top-level scope
    @ none:3
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:385
 [23] macro expansion
    @ /usr/local/lib/R/site-library/JuliaCall/julia/RmdStd.jl:15 [inlined]
 [24] top-level scope
    @ ./none:14
 [25] eval
    @ ./boot.jl:385 [inlined]
 [26] eval_string(x::String)
    @ Main.JuliaCall /usr/local/lib/R/site-library/JuliaCall/julia/setup.jl:203
 [27] docall(call1::Ptr{Nothing})
    @ Main.JuliaCall /usr/local/lib/R/site-library/JuliaCall/julia/setup.jl:176
during initialization of module HDF5_jll
Backtrace:
  1. global .main()
  2. execute(...)
  3. rmarkdown::render(...)
  4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  5. knitr:::process_file(text, output)
     ...
 15. JuliaCall:::stdout_capture_command(buffer)
 16. base::tryCatch(...)
 17. base (local) tryCatchList(expr, classes, parentenv, handlers)
 18. base (local) tryCatchOne(...)
 19. value[[3L]](cond)



Quitting from lines 25-35 [unnamed-chunk-3] (demo.qmd)
Execution halted
Julia exit.

Any ideas @evetion / colleagues?
@Robinlovelace
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The code clearly can run, just not with Quarto? Image below shows great plot from Julia:

image

@Robinlovelace
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Related? Devcontainer boots into recovery mode:

image

@evetion
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evetion commented Sep 23, 2024

This is again Julia finding a shared library from the system (which fails on a version mismatch) earlier then the Julia provided one, because R loaded it. You might try to set the LD_LIBRARY_PATH to empty (or print its contents to check this assumption) before any Julia(Call) invocation.

Relates to JuliaInterop/JuliaCall#234

@Robinlovelace
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Thanks, that's a good basis for debugging. Could it maybe fix actions on Linux if solved also, I wonder...

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@Robinlovelace @evetion