Segmentation fault when calling basic python functions

[johannes-fischer]

Affects: PythonCall

Describe the bug
I get segmentation faults when using PythonCall to call python functions that create python objects many times. It does not happen deterministically, but happens (on a couple of systems I have tested it on) reliably for the MWE below:

using PythonCall
N = 100_000_000
for i in 1:N
    args = pytuple((2.0, 1.0, 0.0))
    @assert !pyeq(Bool, args[0], args[2]) # SEGFAULT
    if i % 100_000 == 0
        println("step $i ($(i/N*100) %)")
    end
end

Sometimes I get the segmentation fault immediately, before the first print statement, sometimes 30% of the loop succedes before the segfault.

If I wrap the doubles in Py objects explicitly before, I do not get segmentation faults:

using PythonCall
N = 100_000_000
for i in 1:N
    args = pytuple((Py(2.0), Py(1.0), Py(0.0)))
    @assert !pyeq(Bool, args[0], args[2]) # NO SEGFAULT
    if i % 100_000 == 0
        println("step $i ($(i/N*100) %)")
    end
end

My understanding is that this shouldn't be necessary to deal with explicitly, but somehow it is in this example. And since this is only a MWE it is not a solution to my actual problem, since I do not know which calls / arguments need this explicit handling and which do not.

Here is the segfault output (from the first code snippet):

[872756] signal 11 (1): Segmentation fault
in expression starting at /home/fischer/dev/jl/PythonCallSegFault/pythoncall_segfault_mwe.jl:5
do_richcompare at /usr/local/src/conda/python-3.12.10/Objects/object.c:815 [inlined]
PyObject_RichCompare at /usr/local/src/conda/python-3.12.10/Objects/object.c:865 [inlined]
PyObject_RichCompareBool at /usr/local/src/conda/python-3.12.10/Objects/object.c:887
PyObject_RichCompareBool at /home/fischer/.julia/packages/PythonCall/L4cjh/src/C/pointers.jl:303
unknown function (ip: 0x7efe9e9fca05)
unknown function (ip: 0x7efe9e9fc699)
unknown function (ip: 0x7efe9e9fc623)
macro expansion at /home/fischer/.julia/packages/PythonCall/L4cjh/src/Core/Py.jl:132 [inlined]
pyeq at /home/fischer/.julia/packages/PythonCall/L4cjh/src/Core/builtins.jl:304 [inlined]
top-level scope at /home/fischer/dev/jl/PythonCallSegFault/pythoncall_segfault_mwe.jl:12
jl_toplevel_eval_flex at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:934
jl_toplevel_eval_flex at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval_in at /cache/build/tester-amdci5-12/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_46879.1 at /home/fischer/.julia/juliaup/julia-1.11.5+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
exec_options at ./client.jl:323
_start at ./client.jl:531
jfptr__start_73430.1 at /home/fischer/.julia/juliaup/julia-1.11.5+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
true_main at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/jlapi.c:900
jl_repl_entrypoint at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/jlapi.c:1059
main at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/cli/loader_exe.c:58
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 312994585 (Pool: 312994469; Big: 116); GC: 13
[1]    872756 segmentation fault  julia pythoncall_segfault_mwe.jl

Your system
Please provide detailed information about your system:

• OS: Ubuntu 20.04

julia> versioninfo()
Julia Version 1.11.5
Commit 760b2e5b739 (2025-04-14 06:53 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 16 × 12th Gen Intel(R) Core(TM) i7-1260P
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, alderlake)
Threads: 1 default, 0 interactive, 1 GC (on 16 virtual cores)

julia> Pkg.status()
Status `~/dev/jl/PythonCallSegFault/Project.toml`
  [992eb4ea] CondaPkg v0.2.29
  [6099a3de] PythonCall v0.9.25

julia> CondaPkg.status()
CondaPkg Status /home/fischer/dev/jl/PythonCallSegFault/CondaPkg.toml (empty)
Environment
  /home/fischer/dev/jl/PythonCallSegFault/.CondaPkg/.pixi/envs/default

julia> pyimport("sys").version
Python: '3.12.10 | packaged by conda-forge | (main, Apr 10 2025, 22:41:16) [GCC 13.3.0]'

Additional context
The actual context where this happened to me is that I am using PythonCall.jl to use the python interface of the lanelet2 library, which in turn is a boost python interface to C++ code. I am getting segmentation faults from a couple of calls to this library.