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JuliaCall segfault (even in fresh enviroment) with Julia 1.12 #748
Description
Affects: JuliaCall
Describe the bug
I had been using JuliaCall for a while.
and today it just stopped working for me.
Python just crashed out, no error or nothing
So I made the most MWE for it. In a fresh environment.
Running:
conda create -n temp -c conda-forge python pip
conda activate temp
pip install juliapkg juliacall
pythonthen running
import juliacall
in python.
the following was the output:
>>> import juliacall
[juliapkg] Found dependencies: /home/frames/miniconda3/envs/temp/lib/python3.14/site-packages/juliacall/juliapkg.json
[juliapkg] Found dependencies: /home/frames/miniconda3/envs/temp/lib/python3.14/site-packages/juliapkg/juliapkg.json
[juliapkg] Locating Julia ^1.10.3
[juliapkg] Using Julia 1.12.5 at /home/frames/.julia/juliaup/julia-1.12.5+0.x64.linux.gnu/bin/julia
[juliapkg] Using Julia project at /home/frames/miniconda3/envs/temp/julia_env
[juliapkg] Writing Project.toml:
| [deps]
| PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
| OpenSSL_jll = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
|
| [compat]
| PythonCall = "=0.9.31"
| OpenSSL_jll = "3.0.0 - 3.6"
[juliapkg] Installing packages:
| import Pkg
| Pkg.Registry.update()
| Pkg.add([
| Pkg.PackageSpec(name="PythonCall", uuid="6099a3de-0909-46bc-b1f4-468b9a2dfc0d"),
| Pkg.PackageSpec(name="OpenSSL_jll", uuid="458c3c95-2e84-50aa-8efc-19380b2a3a95"),
| ])
| Pkg.resolve()
| Pkg.precompile()
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Updating `~/miniconda3/envs/temp/julia_env/Project.toml`
[6099a3de] + PythonCall v0.9.31
[458c3c95] ~ OpenSSL_jll ⇒ v3.5.4+0
Updating `~/miniconda3/envs/temp/julia_env/Manifest.toml`
[992eb4ea] + CondaPkg v0.2.33
[9a962f9c] + DataAPI v1.16.0
[e2d170a0] + DataValueInterfaces v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.7.1
[0f8b85d8] + JSON3 v1.14.3
[1914dd2f] + MacroTools v0.5.16
[0b3b1443] + MicroMamba v0.1.14
[bac558e1] + OrderedCollections v1.8.1
[69de0a69] + Parsers v2.8.3
[fa939f87] + Pidfile v1.3.0
[aea7be01] + PrecompileTools v1.3.3
[21216c6a] + Preferences v1.5.1
[6099a3de] + PythonCall v0.9.31
[6c6a2e73] + Scratch v1.3.0
[856f2bd8] + StructTypes v1.11.0
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.12.1
[e17b2a0c] + UnsafePointers v1.0.0
⌅ [f8abcde7] + micromamba_jll v1.5.12+0
[4d7b5844] + pixi_jll v0.41.3+0
[0dad84c5] + ArgTools v1.1.2
[56f22d72] + Artifacts v1.11.0
[2a0f44e3] + Base64 v1.11.0
[ade2ca70] + Dates v1.11.0
[f43a241f] + Downloads v1.7.0
[7b1f6079] + FileWatching v1.11.0
[b77e0a4c] + InteractiveUtils v1.11.0
[ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
[4af54fe1] + LazyArtifacts v1.11.0
[b27032c2] + LibCURL v0.6.4
[76f85450] + LibGit2 v1.11.0
[8f399da3] + Libdl v1.11.0
[56ddb016] + Logging v1.11.0
[d6f4376e] + Markdown v1.11.0
[a63ad114] + Mmap v1.11.0
[ca575930] + NetworkOptions v1.3.0
[44cfe95a] + Pkg v1.12.1
[de0858da] + Printf v1.11.0
[9a3f8284] + Random v1.11.0
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization v1.11.0
[f489334b] + StyledStrings v1.11.0
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test v1.11.0
[cf7118a7] + UUIDs v1.11.0
[4ec0a83e] + Unicode v1.11.0
[e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
[deac9b47] + LibCURL_jll v8.15.0+0
[e37daf67] + LibGit2_jll v1.9.0+0
[29816b5a] + LibSSH2_jll v1.11.3+1
[14a3606d] + MozillaCACerts_jll v2025.11.4
[458c3c95] ~ OpenSSL_jll ⇒ v3.5.4+0
[83775a58] + Zlib_jll v1.3.1+2
[8e850ede] + nghttp2_jll v1.64.0+1
[3f19e933] + p7zip_jll v17.7.0+0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Precompiling packages finished.
1 dependency successfully precompiled in 14 seconds. 51 already precompiled.
Project No packages added to or removed from `~/miniconda3/envs/temp/julia_env/Project.toml`
Manifest No packages added to or removed from `~/miniconda3/envs/temp/julia_env/Manifest.toml`
Segmentation fault (core dumped)
frames@joseki:~/repos/biohaus2$
Your system
Please provide detailed information about your system:
- The operating system
$ lsb_release -a
No LSB modules are available.
Distributor ID: Linuxmint
Description: Linux Mint 22
Release: 22
Codename: wilm
- The version of Julia, Python, PythonCall, JuliaCall and any other affected packages
Julia: 1.12.5 (also saw on 1.12.1)
Python: 3.14.3
JuliaCall: 0.9.31
julipkg: 0.1.22
- If an issue with JuliaCall, the output of
pip listorconda listandjuliapkg.status().
>>> import juliapkg
>>> juliapkg.status()
JuliaPkg Status
/home/frames/miniconda3/envs/temp/julia_env/pyjuliapkg/juliapkg.json (empty project)
Julia 1.12.5 @ /home/frames/.julia/juliaup/julia-1.12.5+0.x64.linux.gnu/bin/julia
$ pip list
Package Version
--------- -------
filelock 3.20.3
juliacall 0.9.31
juliapkg 0.1.22
pip 26.0.1
semver 3.0.4
tomli 2.4.0
tomlkit 0.13.3
$ conda list
# packages in environment at /home/frames/miniconda3/envs/temp:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 hda65f42_8 conda-forge
ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge
filelock 3.20.3 pypi_0 pypi
icu 78.2 h33c6efd_0 conda-forge
juliacall 0.9.31 pypi_0 pypi
juliapkg 0.1.22 pypi_0 pypi
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
libexpat 2.7.3 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libgcc 15.2.0 he0feb66_17 conda-forge
libgomp 15.2.0 he0feb66_17 conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
libmpdec 4.0.0 hb03c661_1 conda-forge
libsqlite 3.51.2 hf4e2dac_0 conda-forge
libstdcxx 15.2.0 h934c35e_17 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
pip 26.0.1 pyh145f28c_0 conda-forge
python 3.14.3 h32b2ec7_101_cp314 conda-forge
python_abi 3.14 8_cp314 conda-forge
readline 8.3 h853b02a_0 conda-forge
semver 3.0.4 pypi_0 pypi
tk 8.6.13 noxft_h366c992_103 conda-forge
tomli 2.4.0 pypi_0 pypi
tomlkit 0.13.3 pypi_0 pypi
tzdata 2025c hc9c84f9_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
frames@joseki:~/repos/biohaus2$
Activity
oxinabox commentedon Feb 11, 2026
Here is the output of my syslog
oxinabox commentedon Feb 11, 2026
If i do
Then it is fine.
Similar for
~1.11So I guess this is a
~1.12issue.[-]JuliaCall segfault (even in fresh enviroment)[/-][+]JuliaCall segfault (even in fresh enviroment) with Julia 1.12[/+]JamesWrigley commentedon Feb 11, 2026
Do older versions of Python like 3.13 work? There was some issue with 3.14 compatibility though it should've been fixed now.
oxinabox commentedon Feb 11, 2026
No. It also fails on Python 3.12.12
cjdoris commentedon Feb 11, 2026
In python, what is
ssl.OPENSSL_VERSION_INFO?(I just discovered that in CI we are only testing JuliaCall against Julia 1.11 because of OpenSSL incompatibility. Might be your issue too.)
oxinabox commentedon Feb 11, 2026
Where as I see
OpenSSL_jll = "3.0.0 - 3.6"which I am guessing is a different version?
I do not recall how JLLs code for versions
So we might be getting a segfault from trying to load two different version of the shame shared library?
cjdoris commentedon Feb 11, 2026
Oh I know, it'll be the new default number of threads in Julia 1.12. Try running python like
python -X juliacall-threads=1and see if that makes a difference.oxinabox commentedon Feb 12, 2026
Yes, that works fine.