Unclear error (Segmentation Fault) when trying to store `System` as global variable within package

[miles-1]

If you try to make a package that stores the results of a System call as a global variable, the REPL crashes with a "Segmention fault" error (full error message below). I imagine this crash behavior is not intended, even if this structure is not recommended for using Systems. I made an MRE with the following file structure & contents:

project_dir
 ├ HC
 │ ├ src
 │ │ ╰ HC.jl
 │ ├ Manifest.toml
 │ ╰ Project.toml
 ╰ run_model.jl

HC.jl:

module HC

using HomotopyContinuation: @var, System, solve, real_solutions

@var S I
@var r d β μ

export get_eqs

_symbolic_model = System(
    [
        r * (S + I) - d * S - β * S * I,
        β * S * I - (d + μ) * I
    ],
    variables = [S, I],
    parameters = [r, d, β, μ]
)

function get_eqs(
    p_set::Vector{Float64}
)::Vector
    result = solve(
        _symbolic_model,
        target_parameters = p_set,
        show_progress = false,
        threading = false,
    )
    return real_solutions(result)
end

end

run_model.jl:

using HC

for i in 0.1:0.1:0.5
    get_eqs([2, 0.5, 0.5, i])
end

resulting error:

[71867] signal 11 (1): Segmentation fault: 11
in expression starting at /Users/miles/test/run_model.jl:3
_ZNSt3__16__treeINS_12__value_typeIN9SymEngine3RCPIKNS2_5BasicEEES6_EENS_19__map_value_compareIS6_S7_NS2_15RCPBasicKeyLessELb1EEENS_9allocatorIS7_EEE12__find_equalIS6_EERPNS_16__tree_node_baseIPvEERPNS_15__tree_end_nodeISI_EERKT_ at /Users/miles/.julia/artifacts/72bbdc1bf66a1722a793e6fb95d39c18029d3937/lib/libsymengine.0.9.0.dylib (unknown line)
mapbasicbasic_insert at /Users/miles/.julia/artifacts/72bbdc1bf66a1722a793e6fb95d39c18029d3937/lib/libsymengine.0.9.0.dylib (unknown line)
setindex! at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/model_kit/symengine.jl:887
CompiledSystem at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/model_kit/compiled_system_homotopy.jl:32
#MixedSystem#59 at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/systems/mixed_system.jl:13
MixedSystem at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/systems/mixed_system.jl:13 [inlined]
#fixed#80 at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/systems.jl:23
fixed at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/systems.jl:17 [inlined]
#polyhedral#223 at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/polyhedral.jl:174
polyhedral at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/polyhedral.jl:167 [inlined]
#solver_startsolutions#270 at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/solve.jl:161
solver_startsolutions at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/solve.jl:115 [inlined]
solver_startsolutions at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/solve.jl:115 [inlined]
#solve#277 at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/solve.jl:468
solve at /Users/miles/.julia/packages/HomotopyContinuation/Cibx5/src/solve.jl:435
unknown function (ip: 0x10ef5777e)
get_eqs at /Users/miles/test/HC/src/HC.jl:22
top-level scope at /Users/miles/test/run_model.jl:4
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/toplevel.c:934
jl_toplevel_eval_flex at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/toplevel.c:952 [inlined]
ijl_toplevel_eval_in at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
include_string at ./loading.jl:2734
_include at ./loading.jl:2794
include at ./Base.jl:557
jfptr_include_47031.1 at /Users/miles/.julia/juliaup/julia-1.11.5+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
exec_options at ./client.jl:323
_start at ./client.jl:531
jfptr__start_73719.1 at /Users/miles/.julia/juliaup/julia-1.11.5+0.x64.apple.darwin14/lib/julia/sys.dylib (unknown line)
jl_apply at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/./julia.h:2157 [inlined]
true_main at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/jlapi.c:900
jl_repl_entrypoint at /Users/julia/.julia/scratchspaces/a66863c6-20e8-4ff4-8a62-49f30b1f605e/agent-cache/default-grannysmith-C07ZQ07RJYVY.0/build/default-grannysmith-C07ZQ07RJYVY-0/julialang/julia-release-1-dot-11/src/jlapi.c:1059
Allocations: 79930818 (Pool: 79928292; Big: 2526); GC: 36
zsh: segmentation fault  julia run_model.jl

[PBrdng]

Hi, unfortunately I can't reproduce this error. On my computer the code runs smoothly.

On a side note: did you know that you can pass vectors of parameters? In your case, this could look like this:

using HomotopyContinuation

p0 = randn(ComplexF64, 4)
result0 = solve(
        _symbolic_model,
        target_parameters = p0,
        show_progress = false,
        threading = false,
    )

parameters = map(0.1:0.1:0.5) do i
    [2, 0.5, 0.5, i]
end

result = solve(
        _symbolic_model,
        solutions(result0),
        start_parameters = p0,
        target_parameters = parameters,
        show_progress = false,
        threading = false,
    )

If you are only interested in the real solutions, you can add this as an option:

result = solve(
        _symbolic_model,
        solutions(result0),
        start_parameters = p0,
        target_parameters = parameters,
        show_progress = false,
        threading = false,
        transform_result = (r,p) -> real_solutions(r),
    )

[miles-1]

Strange that it isn't working for me. I believe it has to do with precompilation of the HC package, but am not familiar enough with the details there to do more diagnosis, so I'll close this.

I did not know multiple parameter sets could be passed at once, thanks very much for the tip!