`Agents.jl` does not precompile with Julia 1.12.0 (Linux)

[markusgumbel]

I have created an empty Julia project called agents112 and have added the Agents.jl package (version 6.2.10). The precompilation process with Julia 1.12.0 always ends with errors.

Here's the console log:

(agents112) pkg> add Agents
   Resolving package versions...
    Updating `~/Local-Docs/src/Julia/agents112/Project.toml`
  [46ada45e] + Agents v6.2.10
    Updating `~/Local-Docs/src/Julia/agents112/Manifest.toml`
...
       Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
  ✗ JLD2
  ✗ StaticGraphs
  ✗ MetaGraphs
  ✗ LightOSM
  ✗ Agents
Precompiling packages finished.
  0 dependencies successfully precompiled in 74 seconds. 156 already precompiled.
  5 dependencies errored.
  For a report of the errors see `julia> err`. To retry use `pkg> precompile`

The full error stack is

julia> err
PkgPrecompileError: The following 1 direct dependency failed to precompile:

Agents 

Failed to precompile Agents [46ada45e-f475-11e8-01d0-f70cc89e6671] to "/home/markus/.julia/compiled/v1.12/Agents/jl_YUTZy9".
Error encountered while load FileIO.File{FileIO.DataFormat{:JLD2}, String}("/tmp/jl_HGLl4b").

Fatal error:
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading JLD2 using JLD2")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2182
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2190
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2460
  [4] _require_prelocked
    @ ./loading.jl:2459 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:2457
  [7] require
    @ ./loading.jl:2455 [inlined]
  [8] #37
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:203 [inlined]
  [9] lock(f::FileIO.var"#37#38"{Base.PkgId}, l::ReentrantLock)
    @ Base ./lock.jl:335
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:203
 [11] action
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:196 [inlined]
 [12] action
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:185 [inlined]
 [13] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:113
 [14] load
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:109 [inlined]
 [15] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
 [16] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [17] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [18] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [19] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined]
 [20] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:121 [inlined]
 [22] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
Stacktrace:
  [1] handle_error(e::ConcurrencyViolationError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/EI2b8/src/error_handling.jl:75
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/EI2b8/src/error_handling.jl:66
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:228
  [4] action
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:196 [inlined]
  [5] action
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:185 [inlined]
  [6] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:113
  [7] load
    @ ~/.julia/packages/FileIO/EI2b8/src/loadsave.jl:109 [inlined]
  [8] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
  [9] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [10] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [11] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [12] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined]
 [13] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [14] macro expansion
    @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:121 [inlined]
 [15] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
 [16] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [17] IncludeInto
    @ ./Base.jl:308 [inlined]
 [18] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/JLD2.jl:518
 [19] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [20] 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:2997
 [21] top-level scope
    @ stdin:5
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2843
 [24] include_string
    @ ./loading.jl:2853 [inlined]
 [25] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [26] _start()
    @ Base ./client.jl:550
in expression starting at /home/markus/.julia/packages/JLD2/wLPAN/src/precompile.jl:3
in expression starting at /home/markus/.julia/packages/JLD2/wLPAN/src/JLD2.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "/home/markus/.julia/compiled/v1.12/JLD2/jl_l27p8U".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3284
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2652
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3855
 [10] maybe_cachefile_lock
    @ ./loading.jl:3852 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2638
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2465
 [13] macro expansion
    @ ./loading.jl:2393 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2358
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2334
 [17] top-level scope
    @ ~/.julia/packages/StaticGraphs/463Ar/src/StaticGraphs.jl:4
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [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:2997
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2843
 [23] include_string
    @ ./loading.jl:2853 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [25] _start()
    @ Base ./client.jl:550
in expression starting at /home/markus/.julia/packages/StaticGraphs/463Ar/src/StaticGraphs.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile StaticGraphs [4c8beaf5-199b-59a0-a7f2-21d17de635b6] to "/home/markus/.julia/compiled/v1.12/StaticGraphs/jl_AXSMUx".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3284
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2652
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3855
 [10] maybe_cachefile_lock
    @ ./loading.jl:3852 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2638
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2465
 [13] macro expansion
    @ ./loading.jl:2393 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2358
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2334
 [17] top-level scope
    @ ~/.julia/packages/LightOSM/qfooJ/src/LightOSM.jl:9
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [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:2997
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2843
 [23] include_string
    @ ./loading.jl:2853 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [25] _start()
    @ Base ./client.jl:550
in expression starting at /home/markus/.julia/packages/LightOSM/qfooJ/src/LightOSM.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile LightOSM [d1922b25-af4e-4ba3-84af-fe9bea896051] to "/home/markus/.julia/compiled/v1.12/LightOSM/jl_CHaVlU".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3284
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2652
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.0+0.x64.linux.gnu/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3855
 [10] maybe_cachefile_lock
    @ ./loading.jl:3852 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2638
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2465
 [13] macro expansion
    @ ./loading.jl:2393 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2358
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2334
 [17] top-level scope
    @ ~/.julia/packages/Agents/WuWeG/src/spaces/openstreetmap.jl:10
 [18] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:307
 [19] top-level scope
    @ ~/.julia/packages/Agents/WuWeG/src/Agents.jl:45
 [20] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [21] 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)
    @ Base ./loading.jl:2997
 [22] top-level scope
    @ stdin:5
 [23] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2843
 [25] include_string
    @ ./loading.jl:2853 [inlined]
 [26] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [27] _start()
    @ Base ./client.jl:550
in expression starting at /home/markus/.julia/packages/Agents/WuWeG/src/spaces/openstreetmap.jl:3
in expression starting at /home/markus/.julia/packages/Agents/WuWeG/src/Agents.jl:1
in expression starting at stdin:

Julia version:

julia> versioninfo()
Julia Version 1.12.0
Commit b907bd0600f (2025-10-07 15:42 UTC)
Build Info:
  Official https://julialang.org release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 14 × Intel(R) Core(TM) Ultra 7 165U
  WORD_SIZE: 64
  LLVM: libLLVM-18.1.7 (ORCJIT, alderlake)
  GC: Built with stock GC
Threads: 8 default, 1 interactive, 8 GC (on 14 virtual cores)
Environment:
  JULIA_HOME = /home/markus/.juliaup
  JULIA_EDITOR = code
  JULIA_VSCODE_REPL = 1
  JULIA_NUM_THREADS = 8

[markusgumbel]

The stack trace suggests this could be a concurrency problem. However, the error still occurs even if the number of threads is set to 1 (JULIA_NUM_THREADS = 1). Strange.

[Datseris]

I'm not surprised. Most of the packages I use do not work on Julia 1.12 so I haven't moved there... Currently happy and stable with Julia 1.11.

Although this issue could be related to JuliaDynamics/Attractors.jl#167 . Perhaps in the ensemble simulations here we follow the same tactic? But looking at the source code, it doesn't seem like we do. We use pmap:

Agents.jl/src/simulations/ensemblerun.jl

Line 97 in 44ec181

all_data = ProgressMeter.progress_pmap(models; progress) do model

so I am not sure... @Tortar have you moved to Julia 1.12 by any chance?

[Datseris]

thanks for reporting this by the way! If you know how to fix it please do consider a PR!

[markusgumbel]

I'm not surprised. Most of the packages I use do not work on Julia 1.12 so I haven't moved there... Currently happy and stable with Julia 1.11.

That's true. I was playing with the new compiler (juliac). With Julia 1.11 and PackageCompiler it was possible for me to create a distributable package that uses Agents.jl, though quite large.

[markusgumbel]

thanks for reporting this by the way! If you know how to fix it please do consider a PR!

I'll try. But it seems to be a general Julia compile issue - let's see...

[Datseris]

That's true. I was playing with the new compiler (juliac). With Julia 1.11 and PackageCompiler it was possible for me to create a distributable package that uses Agents.jl, though quite large.

Oh wow, that is great news and very interesting! Would you be willing to contribute a section in the documentation about this?

What size are we talking about out of interest?

[Tortar]

No, I haven't tried with 1.12. Though, it's very probably a Julia problem, I would wait a new release before trying again

[markusgumbel]

Oh wow, that is great news and very interesting! Would you be willing to contribute a section in the documentation about this?
What size are we talking about out of interest?

The size is 2.2 G in total.

$ du -h -d 1 .
52K	./bin
3,0M	./libexec
1,2G	./lib
1023M	./share
2,2G	.

It's an agent based SIR simulation (https://en.wikipedia.org/wiki/Compartmental_models_(epidemiology)#The_SIR_model) with Makie UI (abmplot()), mainly for educational purposes.

Yes, I could contribute a section. Basically, it's just a single Julia script like this (though there a lot of constraints to consider):

using PackageCompiler
using SIRmod

create_app("src/Julia/SIRmod", "src/Julia/SIRmodCompiled";
    filter_stdlibs = false,
    incremental = true,
    force = true,
    precompile_execution_file = "src/Julia/SIRRep.jl",
)

Could you give some advice where such a documentation should go? Probably we could take a model from the zoo as a show case?

[Datseris]

I think the best place for this is to be a brand new documentation page at the top level, right after "Developers Docs". I think for this page it is probably best to just make the model from scratch in the page if it is not too large. The docs do have an SIR model already: https://juliadynamics.github.io/Agents.jl/stable/examples/sir/ so we can reference that page for details of how the model works, etc.

I agree that 2.2GB sounds excessive for such a simple thing, but on the other hand it is baking the entirety of GLMakie into it, so I can't gauge how large size such a standalone GUI app would be if made in C

[JonasIsensee]

The problem is this:
On julia 1.12 in a temp environment installing Agents gives an ancient JLD2 version that is not compatible with julia v1.12.

The problem is Agents -> LightOSM -> MetaGraphs (compat v0.7 but latest is v0.8) -> JLD2 (old compat bound, latest MetaGraphs is compatible with latest JLD2)

Solution -> get LightOSM to bump their compat bounds on MetaGraphs

[markusgumbel]

Thank you for this hint. Here's a Github issue for LightOSM reporting that it does not compile on Julia 1.12: DeloitteOptimalReality/LightOSM.jl#111 (comment)

[JonasIsensee]

LightOSM appears to be abandoned.

I went the quickest route and added a backport release to the JLD2 v0.4 series to make it work on julia v1.12.

(This issue can be marked as completed)