Module files that import LightGBM fail to compile

[msekino]

I'd like to use LightGBM in a module file.
I made a project "Example" and wrote a following code in Example.jl

module Example
using LightGBM
end

using Example resulted in the following.

┌ Info: Precompiling Example [9e033b86-410e-4dd2-a032-f2c9367e52e7]
└ @ Base loading.jl:1278
ERROR: LoadError: InitError: Evaluation into the closed module `LightGBM` breaks incremental compilation because the side effects will not be permanent. This is likely due to some other module mutating `LightGBM` with `include` during precompilation - don't do this.
Stacktrace:
...

Temporarily, it is possible to avoid the error by putting __precompile__(false) to the beginning of the file, but it doesn't seem to be a very preferred solution.

[yalwan-iqvia]

Hi @msekino ! Thanks for taking the time to report this

After a quick bit of digging it seems it is due to this:

LightGBM.jl/src/LightGBM.jl

Line 21 in 47d9a87

include(joinpath(@__DIR__, "MLJInterface.jl"))

I'll have to figure out why I did it and then stop doing it without breaking it. I will keep you up to date with this. Hopefully the fix can make it soon.

[yalwan-iqvia]

WARNING: eval into closed module MLJModelInterface:
:Bool
  ** incremental compilation may be fatally broken for this module **

WARNING: eval into closed module MLJModelInterface:
:Bool
  ** incremental compilation may be fatally broken for this module **

WARNING: eval into closed module MLJModelInterface:
:Bool
  ** incremental compilation may be fatally broken for this module **

WARNING: eval into closed module MLJModelInterface:
:Bool
  ** incremental compilation may be fatally broken for this module **

I think I did it to stop this class of warnings appearing. However, it seems like its no consequence for me to remove this include from the init, which would fix the issue. I will go to MLJ project and see what I can do to suppress those warnings.

I will try to come with a fix soon.

[yalwan-iqvia]

@ablaom do you know what I might do in order to stop those warnings appearing?

[ablaom]

Yeah, I've also had problems using eval(and hence macros) inside an __init__ function (see JuliaAI/MLJModels.jl#74). What's the reason for including the file MLJInterface.jl post facto ? If you move it out of __init__ I expect the warnings will go away.

Maybe this helps: JuliaLang/julia#29059 .

[yalwan-iqvia]

Sorry, I was a little unclear. I was asking because it occurs when I move it out of __init__

[ablaom]

Oh, I see. This looks like a problem with MLJModelInterface.jl.

My guess is there is an issue with metadata_pkg and metadata_model methods, which have eval in them. Maybe something to do with use of parentmodule, but I'm not sure and not completely understanding why this has not come up with other interfaces. I will investigate. cc @tlienart

Would be helpful to know if you get the warnings if you remove the module wrapping of the code in MLJlInterface.jl.

If my suspicions are right, a solution for you might be to replace the calls to metadata_pkg and metadata_model with explicit trait definitions. (Personally, I prefer this anyhow). See the attached screenshot, which is from https://alan-turing-institute.github.io/MLJ.jl/dev/adding_models_for_general_use/#Trait-declarations-1

[yalwan-iqvia]

I managed to find this:

https://discourse.julialang.org/t/use-of-eval-in-closed-module-and-incremental-compilation-may-be-broken/30028

Is it possible that is related?

[yalwan-iqvia]

https://github.com/alan-turing-institute/MLJModelInterface.jl/blob/master/src/model_def.jl#L70
This the possible culprit?

[ablaom]

Yes that's it. Good catch. This needs to be evaluated in the module from where the @mlj_macro is called, which must according be passed to the function you point out as an argument.

Working on a new release of MLJModelsInterface. Thanks for bringing this to my attention.

[ablaom]

@msekino When JuliaRegistries/General#22970 is merged, would you be so kind as to update your project env and confirm that my fix resolves your issue?

[ablaom]

Oh sorry. @yalwan-iqvia will first need to move the include out of __init__ for this to work.

[msekino]

@ablaom Thank you for your help!

I just updated as follows.

(@v1.5) pkg> up
   Updating registry at `C:\Users\msekino\.julia\registries\General`
  Installed MLJModelInterface ─ v0.3.6
  ...
Updating `C:\Users\msekino\.julia\environments\v1.5\Project.toml`
  ...
Updating `C:\Users\msekino\.julia\environments\v1.5\Manifest.toml`
  [e80e1ace] ↑ MLJModelInterface v0.3.5 ⇒ v0.3.6
  ...

I made a project "Example"

julia> using PkgTemplates
[ Info: Precompiling PkgTemplates [14b8a8f1-9102-5b29-a752-f990bacb7fe1]

julia> t = Template(user = "msekino")
  ...

julia> t("Example")
  ...

then, I wrote Example.jl

module Example
using LightGBM
end

However, using Example resulted in the following.

julia> using Example
[ Info: Precompiling Example [400a67cc-5385-4025-bc17-a97de4bd9e1e]
ERROR: LoadError: InitError: Evaluation into the closed module `LightGBM` breaks incremental compilation because the side effects will not be permanent. This is likely due to some other module mutating `LightGBM` with `include` during precompilation - don't do this.
Stacktrace:
 [1] include(::Function, ::Module, ::String) at .\Base.jl:380
 [2] include at .\Base.jl:368 [inlined]
 [3] include at C:\Users\msekino\.julia\packages\LightGBM\3uotD\src\LightGBM.jl:1 [inlined]
 [4] __init__() at C:\Users\msekino\.julia\packages\LightGBM\3uotD\src\LightGBM.jl:21
 [5] _include_from_serialized(::String, ::Array{Any,1}) at .\loading.jl:697
 [6] _require_from_serialized(::String) at .\loading.jl:749
 [7] _require(::Base.PkgId) at .\loading.jl:1040
 [8] require(::Base.PkgId) at .\loading.jl:928
 [9] require(::Module, ::Symbol) at .\loading.jl:923
 [10] include(::Function, ::Module, ::String) at .\Base.jl:380
 [11] include(::Module, ::String) at .\Base.jl:368
 [12] top-level scope at none:2
 [13] eval at .\boot.jl:331 [inlined]
 [14] eval(::Expr) at .\client.jl:467
 [15] top-level scope at .\none:3
during initialization of module LightGBM
in expression starting at D:\workspace\private\Julia\Example\src\Example.jl:3
ERROR: Failed to precompile Example [400a67cc-5385-4025-bc17-a97de4bd9e1e] to C:\Users\msekino\.julia\compiled\v1.5\Example\UxrAa_P2WnP.ji.
Stacktrace:
 [1] error(::String) at .\error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at .\loading.jl:1305
 [3] _require(::Base.PkgId) at .\loading.jl:1030
 [4] require(::Base.PkgId) at .\loading.jl:928
 [5] require(::Module, ::Symbol) at .\loading.jl:923

I'm not sure what caused it. And I'm sorry if I'm doing something wrong...

[yalwan-iqvia]

@msekino hey sorry for the confusion. What's going on here is that @ablaom has made a fix to an upstream project which I will test now and then make a release. So you'll need an updated version of LightGBM.jl (which I am working on now)

[yalwan-iqvia]

@ablaom I've done this but do you think there might be a better way?
58661c6

[yalwan-iqvia]

@msekino when this merge is complete JuliaRegistries/General#22979

it should hopefully resolve your issue. You will need to make sure to update to LightGBM.jl >= 0.3.2

[msekino]

@yalwan-iqvia @ablaom
Now I was able to precompile the module without problems!
Thank you very much for the quick resolution!

[yalwan-iqvia]

Thanks for reporting and thanks Anthony for the super quick response 😄

[ablaom]

@ablaom I've done this but do you think there might be a better way?
58661c6

Nope. That's the way to do it.