Open
Description
Describe the bug 🐞
When I create a SDEProblem from a SDEFunction I built via a SDESystem I get sefault when trying to solve an EnsembleProblem for large enough trajectories. Bug does not happen if I build the SDEProblem directly from a SDESystem or ReactionSystem.
Expected behavior
I should not get a segfault.
Minimal Reproducible Example 👇
using Catalyst, StochasticDiffEq, ModelingToolkit, SciMLBase
using ModelingToolkit: t_nounits as t, D_nounits as D
@parameters c1 c2
@variables X(t) Y(t)
eqs = [D(X) ~ -c1*X + c2*Y,
D(Y) ~ c1*X - c2*Y]
noiseeqs = [-sqrt(abs(c1*X)) sqrt(abs(c2*Y));
sqrt(abs(c1*X)) -sqrt(abs(c2*Y))]
@named sdesys = SDESystem(eqs, noiseeqs, t, [X, Y], [c1, c2]; tspan = (0, 1000.0))
sdesys = complete(sdesys)
# SDESystem via Catalyst
rn = @reaction_network begin
@species X(t)=50.0 Y(t)=100.0
c1, X --> Y
c2, Y --> X
end
u0 = [X => 50.0, Y => 100.0]
ps = [c1 => 0.5, c2 => 1.0]
sdefun = SDEFunction(sdesys, first.(u0), first.(ps))
sdefun = SDEFunction(sdesys, first.(u0), first.(ps))
sprob_fun = SDEProblem(sdefun, last.(u0), [0.0, 10.0], last.(ps))
sprob_sys = SDEProblem(rn, u0, [0.0, 10.0], ps)
sprob_rn = SDEProblem(sdesys, u0, [0.0, 10.0], ps)
#=
This section works as expected
eprob = EnsembleProblem(sprob_sys)
sol = solve(eprob, EM(), EnsembleSerial(), trajectories = 1000, saveat = 1:10, dt = 1e-3)
eprob = EnsembleProblem(sprob_rn)
sol = solve(eprob, EM(), EnsembleSerial(), trajectories = 1000, saveat = 1:10, dt = 1e-3)
=#
eprob = EnsembleProblem(sprob_fun)
sol = solve(eprob, EM(), EnsembleSerial(), trajectories = 10000, saveat = 1:10, dt = 1e-3)Error & Stacktrace
[14149] signal 11 (128): Segmentation fault
in expression starting at /home/perssos/Dropbox/PhD/tmp/test_fail/MVE.jl:37
gc_mark_outrefs at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:2784 [inlined]
gc_mark_loop_serial_ at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:2946
gc_mark_loop_serial at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:2969
gc_mark_loop at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:3151 [inlined]
_jl_gc_collect at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:3540
ijl_gc_collect at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:3901
maybe_collect at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:922 [inlined]
jl_gc_pool_alloc_inner at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:1327
jl_gc_pool_alloc_noinline at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:1394 [inlined]
jl_gc_alloc_ at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/julia_internal.h:523 [inlined]
jl_gc_alloc at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/gc.c:3954
_new_genericmemory_ at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/genericmemory.c:56
jl_genericmemory_copy_slice at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/genericmemory.c:350
copy at ./array.jl:350 [inlined]
safecopy at /home/perssos/.julia/packages/ResettableStacks/lP2VI/src/core.jl:27 [inlined]
_broadcast_getindex_evalf at ./broadcast.jl:678 [inlined]
_broadcast_getindex at ./broadcast.jl:651 [inlined]
#17 at ./broadcast.jl:1102 [inlined]
ntuple at ./ntuple.jl:50 [inlined]
copy at ./broadcast.jl:1102 [inlined]
materialize at ./broadcast.jl:872 [inlined]
copyat_or_push! at /home/perssos/.julia/packages/ResettableStacks/lP2VI/src/core.jl:35
setup_next_step! at /home/perssos/.julia/packages/DiffEqNoiseProcess/Moaax/src/noise_interfaces/noise_process_interface.jl:174 [inlined]
setup_next_step! at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/integrators/integrator_utils.jl:2 [inlined]
#__init#108 at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:682
__init at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:18 [inlined]
__init at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:18 [inlined]
#__solve#107 at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:6
__solve at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:1 [inlined]
__solve at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:1 [inlined]
__solve at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:1 [inlined]
__solve at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:1 [inlined]
__solve at /home/perssos/.julia/packages/StochasticDiffEq/OmgKe/src/solve.jl:1 [inlined]
#solve_call#35 at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:635
solve_call at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:592 [inlined]
#solve_up#44 at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:1142 [inlined]
solve_up at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:1120 [inlined]
#solve#42 at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:1057 [inlined]
solve at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:1047 [inlined]
#batch_func#681 at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:193 [inlined]
batch_func at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:180 [inlined]
#690 at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:252
unknown function (ip: 0x77f5cab7e0ac)
responsible_map at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:245
#solve_batch#689 at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:251 [inlined]
solve_batch at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:250 [inlined]
macro expansion at ./timing.jl:421 [inlined]
#679 at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:146
with_logstate at ./logging/logging.jl:522
with_logger at ./logging/logging.jl:632 [inlined]
#__solve#678 at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:130
__solve at /home/perssos/.julia/packages/SciMLBase/elLNZ/src/ensemble/basic_ensemble_solve.jl:122 [inlined]
#solve#46 at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:1158 [inlined]
solve at /home/perssos/.julia/packages/DiffEqBase/HyX7M/src/solve.jl:1155
unknown function (ip: 0x77f5cab603a2)
jl_apply at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
do_call at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/interpreter.c:126
eval_value at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/interpreter.c:223
eval_stmt_value at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/interpreter.c:174 [inlined]
eval_body at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/interpreter.c:666
jl_interpret_toplevel_thunk at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/interpreter.c:824
jl_toplevel_eval_flex at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/toplevel.c:943
jl_toplevel_eval_flex at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval_in at /cache/build/builder-amdci5-5/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_46865.1 at /home/perssos/.julia/juliaup/julia-1.11.4+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
exec_options at ./client.jl:323
_start at ./client.jl:531
jfptr__start_73560.1 at /home/perssos/.julia/juliaup/julia-1.11.4+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
true_main at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/jlapi.c:900
jl_repl_entrypoint at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/src/jlapi.c:1059
main at /cache/build/builder-amdci5-5/julialang/julia-release-1-dot-11/cli/loader_exe.c:58
unknown function (ip: 0x77f62b42a1c9)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 65015280 (Pool: 65013556; Big: 1724); GC: 30
Segmentation fault (core dumped)
Environment (please complete the following information):
- Output of
using Pkg; Pkg.status()
[479239e8] Catalyst v14.4.1
[961ee093] ModelingToolkit v9.68.1
[0bca4576] SciMLBase v2.79.0
[789caeaf] StochasticDiffEq v6.74.1- Output of
using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
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[bea87d4a] SuiteSparse_jll v7.7.0+0
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[8e850b90] libblastrampoline_jll v5.11.0+0
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[3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`- Output of
versioninfo()
Julia Version 1.11.4
Commit 8561cc3d68d (2025-03-10 11:36 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-16.0.6 (ORCJIT, alderlake)
Threads: 1 default, 0 interactive, 1 GC (on 14 virtual cores)
Environment:
JULIA_EDITOR = code
JULIA_NUM_THREADS = Additional context
The crash happens only if I simulate many trajectories (trajectories >= 10000).