IJulia world age problem when precompilation is triggered (no method matching `pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})`) #51280

svilupp · 2023-09-12T10:37:03Z

I wanted to cross-link an issue with IJulia that seems to be affecting 1.10 and 1.11-DEV. This seems to also affect any documentation/report tools that use IJulia execution under the hood (eg, Quarto).

When a package needs precompilation, IJulia will throw the following error:

MethodError: no method matching pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})
The applicable method may be too new: running in world age 31373, while current world is 31593.

I can replicate this error on Julia 1.10 beta1, 1.10 beta2 and 1.11 (latest main).
1.9.3 works as expected.

MWE:

Create a mock module in your temp environment

module ABC

greet() = print("Hello World!")

struct A1 end
struct B1 end

greet(::A1) = print("Hello World!")

x(::A1) = "x"

end # module ABC

Add the packages to the project env
Create an Ipython notebook with the following cells

using Pkg; Pkg.activate(".")
using StatsPlots # it can help to have some complex package there to trigger the precompilation more often (to get the error)
using ABC

If precompilation is triggered by adding or Pkg.precompile(), it seems to work
To trigger the error, make some changes in the ABC module that will trigger recompilation (add a new struct and function)
When you try to execute the cell with using ABC, the error will be thrown

Versions:

IJulia version: latest (1.24.2)

Versioninfo:

Julia Version 1.10.0-beta2
Commit a468aa1 (2023-08-17 06:27 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 8 × Apple M1 Pro
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 1 on 6 virtual cores

The text was updated successfully, but these errors were encountered:

vtjnash · 2023-09-12T13:00:31Z

Sounds like 614d917 / 59bf9e8 (#49525) @KristofferC

svilupp · 2023-09-12T19:00:29Z

Wow, this is spot on.

I've just tested the bug on 59bf9e8 and it indeed fails.

I've tried also one commit before it ("feaea2266eabe3d6714e8073ec57cb6bbf14e8ee") and everything works as expected. That saved me a lot of bisecting!

KristofferC · 2023-09-19T14:54:07Z

I'm having issues reproducing this because I cannot seem to get IJulia to work on 1.10... Trying to repro it with something like:

let
Base.PKG_PRECOMPILE_HOOK[] = Returns(nothing)

struct IJuliaStdio{IO_t <: IO} <: Base.AbstractPipe
    io::IOContext{IO_t}
end
IJuliaStdio(io::IO, stream::AbstractString="unknown") =
    IJuliaStdio{typeof(io)}(IOContext(io, :color=>Base.have_color,
                            :jupyter_stream=>stream,
                            :displaysize=>displaysize()))
Base.pipe_reader(io::IJuliaStdio) = io.io.io
Base.pipe_writer(io::IJuliaStdio) = io.io.io
Base.lock(io::IJuliaStdio) = lock(io.io.io)
Base.unlock(io::IJuliaStdio) = unlock(io.io.io)
Base.in(key_value::Pair, io::IJuliaStdio) = in(key_value, io.io)
Base.haskey(io::IJuliaStdio, key) = haskey(io.io, key)
Base.getindex(io::IJuliaStdio, key) = getindex(io.io, key)
Base.get(io::IJuliaStdio, key, default) = get(io.io, key, default)
Base.displaysize(io::IJuliaStdio) = displaysize(io.io)
Base.unwrapcontext(io::IJuliaStdio) = Base.unwrapcontext(io.io)
Base.setup_stdio(io::IJuliaStdio, readable::Bool) = Base.setup_stdio(io.io.io, readable)

redirect_stdout(IJuliaStdio(stdout,"stdout"))
redirect_stderr(IJuliaStdio(stderr,"stderr"))

using ABC
end

doesn't reproduce.

KristofferC · 2023-09-19T15:51:01Z

My assumption was that this came from the logging macro outputting [ Info: Precompiling ABC... but the logging macros have an invokelatest now I see so this can't really be the reason.

svilupp · 2023-09-19T16:03:42Z

When you say you can't get IJulia to work on 1.10, do you mean installing a kernel to run the notebook on?

I tried your example and it indeed works fine.
I've also tried an example closer to what IJulia does with PipeEndpoint (I have no idea what I'm doing), but I cannot repro via REPL:

My attempt

using IJulia: IJuliaStdio

read_stdout = Ref{Base.PipeEndpoint}()
read_stderr = Ref{Base.PipeEndpoint}()

read_stdout[], = redirect_stdout()
redirect_stdout(IJuliaStdio(stdout, "stdout"))
read_stderr[], = redirect_stderr()
redirect_stderr(IJuliaStdio(stderr, "stderr"))

using ABC

using Pkg;
Pkg.precompile(; io=read_stdout[]);

But when I just open a Jupyter Notebook with 1.10 kernel, it's enough to do using ABC to get the error.

I have no idea what I'm looking at, but from the stack trace I would assume it's coming from the nested call to unpack the registry:
~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:261

Pipe leak perhaps?

Stacktrace:

MethodError: no method matching pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})
The applicable method may be too new: running in world age 31373, while current world is 31390.

Closest candidates are:
pipe_writer(::IJulia.IJuliaStdio) (method too new to be called from this world context.)
@ IJulia ~/.julia/packages/IJulia/Vo51o/src/stdio.jl:15
pipe_writer(::Base.ProcessChain)
@ Base process.jl:36
pipe_writer(::Base.Process)
@ Base process.jl:22
...

Stacktrace:
[1] setup_stdio(stdio::IJulia.IJuliaStdio{Base.PipeEndpoint}, readable::Bool)
@ Base ./process.jl:260
[2] setup_stdios(f::Base.var"#784#785"{Cmd}, stdios::Vector{Union{RawFD, IO}})
@ Base ./process.jl:221
[3] _spawn
@ Base ./process.jl:138 [inlined]
[4] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
@ Base ./process.jl:393
[5] open (repeats 2 times)
@ Base ./process.jl:383 [inlined]
[6] open(::Pkg.Registry.var"#19#22"{IOBuffer, Vector{UInt8}, Dict{String, String}}, ::Cmd; kwargs::@kwargs{})
@ Base ./process.jl:415
[7] open
@ Base ./process.jl:414 [inlined]
[8] uncompress_registry(tar_gz::String)
@ Pkg.Registry ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:261
[9] Pkg.Registry.RegistryInstance(path::String)
@ Pkg.Registry ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:328
[10] reachable_registries(; depots::Vector{String})
@ Pkg.Registry ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:434
[11] reachable_registries
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:404 [inlined]
[12] Context
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Types.jl:395 [inlined]
[13] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::IJulia.IJuliaStdio{Base.PipeEndpoint}, kwargs::@kwargs{_from_loading::Bool})
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:150
[14] precompile
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
[15] #precompile#114
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
[16] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1957
[17] __require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1806
[18] #invoke_in_world#3
@ Base ./essentials.jl:921 [inlined]
[19] invoke_in_world
@ Base ./essentials.jl:918 [inlined]
[20] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1797
[21] macro expansion
@ Base ./loading.jl:1784 [inlined]
[22] macro expansion
@ Base ./lock.jl:267 [inlined]
[23] __require(into::Module, mod::Symbol)
@ Base ./loading.jl:1747
[24] #invoke_in_world#3
@ Base ./essentials.jl:921 [inlined]
[25] invoke_in_world
@ Base ./essentials.jl:918 [inlined]
[26] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1740

KristofferC · 2023-09-19T16:08:47Z

I have no idea what I'm looking at, but from the stack trace I would assume it's coming from the nested call to unpack the registry:
~/.julia/juliaup/julia-1.10.0-beta2+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:261

That stacktrace is useful, thanks.

Fixes #51280.

Fixes #51280. (cherry picked from commit c22adc0)

svilupp · 2023-10-12T09:37:27Z

@KristofferC, Can we please re-open this issue?

It seems to be fixed on 1.11#main, but the error still shows up in 1.10 beta3.

Based on the stack trace (see below), it's coming from exactly the same place (registry update -> unpacking the tar.gz in a process).
Has the fix been backported?

Same test setup as before. Adding Pkg.precompile(); at the top, removes the error.

Stack trace:

MethodError: no method matching pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})
The applicable method may be too new: running in world age 31405, while current world is 31583.

Closest candidates are:
pipe_writer(::IJulia.IJuliaStdio) (method too new to be called from this world context.)
@ IJulia ~/.julia/packages/IJulia/Vo51o/src/stdio.jl:15
pipe_writer(::Base.ProcessChain)
@ Base process.jl:36
pipe_writer(::Base.Process)
@ Base process.jl:22
...

Stacktrace:
[1] setup_stdio(stdio::IJulia.IJuliaStdio{Base.PipeEndpoint}, readable::Bool)
@ Base ./process.jl:260
[2] setup_stdios(f::Base.var"#784#785"{Cmd}, stdios::Vector{Union{RawFD, IO}})
@ Base ./process.jl:221
[3] _spawn
@ Base ./process.jl:138 [inlined]
[4] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
@ Base ./process.jl:393
[5] open (repeats 2 times)
@ Base ./process.jl:383 [inlined]
[6] open(::Pkg.Registry.var"#19#22"{IOBuffer, Vector{UInt8}, Dict{String, String}}, ::Cmd; kwargs::@kwargs{})
@ Base ./process.jl:415
[7] open
@ Base ./process.jl:414 [inlined]
[8] uncompress_registry(tar_gz::String)
@ Pkg.Registry ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:261
[9] Pkg.Registry.RegistryInstance(path::String)
@ Pkg.Registry ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:328
[10] reachable_registries(; depots::Vector{String})
@ Pkg.Registry ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:434
[11] reachable_registries
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:404 [inlined]
[12] Context
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/Types.jl:406 [inlined]
[13] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::IJulia.IJuliaStdio{Base.PipeEndpoint}, kwargs::@kwargs{_from_loading::Bool})
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:150
[14] precompile
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
[15] #precompile#114
@ Pkg.API ~/.julia/juliaup/julia-1.10.0-beta3+0.aarch64.apple.darwin14/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
[16] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1957
[17] __require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1806
[18] #invoke_in_world#3
@ Base ./essentials.jl:921 [inlined]
[19] invoke_in_world
@ Base ./essentials.jl:918 [inlined]
[20] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1797
[21] macro expansion
@ Base ./loading.jl:1784 [inlined]
[22] macro expansion
@ Base ./lock.jl:267 [inlined]
[23] __require(into::Module, mod::Symbol)
@ Base ./loading.jl:1747
[24] #invoke_in_world#3
@ Base ./essentials.jl:921 [inlined]
[25] invoke_in_world
@ Base ./essentials.jl:918 [inlined]
[26] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1740
LoadError: MethodError: no method matching pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})
The applicable method may be too new: running in world age 31405, while current world is 31583.

Closest candidates are:
pipe_writer(::IJulia.IJuliaStdio) (method too new to be called from this world context.)
@ IJulia ~/.julia/packages/IJulia/Vo51o/src/stdio.jl:15
pipe_writer(::Base.ProcessChain)
@ Base process.jl:36
pipe_writer(::Base.Process)
@ Base process.jl:22
...

Versioninfo

Julia Version 1.10.0-beta3
Commit 404750f (2023-10-03 12:53 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 8 × Apple M1 Pro
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 8 on 6 virtual cores
Environment:
JULIA_EDITOR = code
JULIA_NUM_THREADS = 8

KristofferC · 2023-10-12T09:43:09Z

This didn't make beta3 so will be in next pre release.

Fixes #51280. (cherry picked from commit c22adc0)

vtjnash added the regression Regression in behavior compared to a previous version label Sep 12, 2023

vtjnash modified the milestones: 1.11, 1.10 Sep 12, 2023

KristofferC self-assigned this Sep 12, 2023

KristofferC mentioned this issue Sep 19, 2023

call Pkg precompile hook in latest world #51397

Merged

KristofferC closed this as completed in #51397 Sep 20, 2023

KristofferC added a commit that referenced this issue Sep 20, 2023

call Pkg precompile hook in latest world (#51397)

c22adc0

Fixes #51280.

KristofferC added a commit that referenced this issue Oct 3, 2023

call Pkg precompile hook in latest world (#51397)

0c39aef

Fixes #51280. (cherry picked from commit c22adc0)

svilupp mentioned this issue Oct 9, 2023

[BUG] IJuliaExt causes problems with IJulia in default environment JuliaPlots/Plots.jl#4719

Closed

nalimilan pushed a commit that referenced this issue Nov 5, 2023

call Pkg precompile hook in latest world (#51397)

17d4bba

Fixes #51280. (cherry picked from commit c22adc0)

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IJulia world age problem when precompilation is triggered (no method matching `pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})`) #51280

IJulia world age problem when precompilation is triggered (no method matching `pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})`) #51280

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IJulia world age problem when precompilation is triggered (no method matching pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})) #51280

IJulia world age problem when precompilation is triggered (no method matching pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})) #51280

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KristofferC commented Oct 12, 2023

IJulia world age problem when precompilation is triggered (no method matching `pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})`) #51280

IJulia world age problem when precompilation is triggered (no method matching `pipe_writer(::IJulia.IJuliaStdio{Base.PipeEndpoint})`) #51280

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