Crashes with Julia 1.12 and Revise.jl

[fabmazz]

I have been using PyPlot (with PyCall) with Revise.jl quite well in the past years, but after the upgrade to Julia 1.12 I see now constant crashes. I've tried to debug these, but they happen quite randomly. I was about to point the issue as happening only in IJulia kernels, when I started seeing them in Julia REPL as well.

These crashes can happen whenever, and are not related to calling "plot" functions.

I have tried reinstalling PyCall and PyPlot with ENV["PYTHON"] = "" (today) and verified the installation happens with a clean Conda.jl environment.

Here is an example of simple commands that trigger the crash:

$ julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.12.3 (2025-12-15)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org release
|__/                   |

julia> using Base.Threads

julia> threadpool()
:interactive

julia> nthreads()
1

julia> Threads.nthreads(:default)
1

julia> using Revise

julia> using PyPlot

[857707] signal 11 (1): Segmentation fault
in expression starting at REPL[6]:1
_PyInterpreterState_GET at /usr/local/src/conda/python-3.12.12/Include/internal/pycore_pystate.h:133 [inlined]
notify_code_watchers at /usr/local/src/conda/python-3.12.12/Objects/codeobject.c:32
code_dealloc at /usr/local/src/conda/python-3.12.12/Objects/codeobject.c:1705
pydecref_ at /home/mazza/.julia/packages/PyCall/1gn3u/src/PyCall.jl:118 [inlined]
pydecref at /home/mazza/.julia/packages/PyCall/1gn3u/src/PyCall.jl:123
jfptr_pydecref_8808 at /home/mazza/.julia/compiled/v1.12/PyCall/GkzkC_o0cEr.so (unknown line)
run_finalizer at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/gc-common.c:180
jl_gc_run_finalizers_in_list at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/gc-common.c:270
run_finalizers at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/gc-common.c:316
ijl_gc_collect at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/gc-stock.c:3483
maybe_collect at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/gc-stock.c:349 [inlined]
ijl_gc_managed_malloc at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/gc-stock.c:3811
jl_alloc_genericmemory_unchecked at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/genericmemory.c:38
_new_genericmemory_ at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/genericmemory.c:68 [inlined]
jl_alloc_genericmemory at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/genericmemory.c:101
ijl_array_grow_end at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/array.c:222
_append_symbol_to_bindings_array at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/module.c:1958 [inlined]
append_module_names at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/module.c:1980
ijl_module_names at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/module.c:2001
#unsorted_names#4 at ./runtime_internals.jl:119 [inlined]
unsorted_names at ./runtime_internals.jl:119 [inlined]
#names#3 at ./runtime_internals.jl:118 [inlined]
names at ./runtime_internals.jl:118 [inlined]
_subtypes_in! at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/InteractiveUtils/src/InteractiveUtils.jl:266
subtypes at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/usr/share/julia/stdlib/v1.12/InteractiveUtils/src/InteractiveUtils.jl:303 [inlined]
_foreach_subtype! at /home/mazza/.julia/packages/Revise/icvyF/src/visit.jl:43
_foreach_subtype! at /home/mazza/.julia/packages/Revise/icvyF/src/visit.jl:49
_foreach_subtype! at /home/mazza/.julia/packages/Revise/icvyF/src/visit.jl:49
foreach_subtype at /home/mazza/.julia/packages/Revise/icvyF/src/visit.jl:38 [inlined]
#__init__##2 at /home/mazza/.julia/packages/Revise/icvyF/src/packagedef.jl:1658
unknown function (ip: 0x7f711c6a894f) at (unknown file)
jl_apply at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined]
start_task at /cache/build/tester-amdci4-9/julialang/julia-release-1-dot-12/src/task.c:1249
Allocations: 5202189 (Pool: 5202112; Big: 77); GC: 7
Segmentation fault (core dumped)

[yuyichao]

I’ve seen these happen without revise when the finalizer runs on a thread that python isnt aware of.

[axsk]

Just coming back to Julia after a christmas break, updated to 1.12.4, and was immediately greeted with exactly this as well :(
Just for reference, as this might be related: #1090

Only workaround that works so far for me: julia --threads=1...

[axsk]

I also seemingly randombly obtained this variation of this error

Error

Fatal Python error: PyThreadState_Get: the function must be called with the GIL held, after Python initialization and before Python finalization, but the GIL is released (the current Python thread state is NULL)                                      |  ETA: 0:03:22        
Python runtime state: initialized1 ns                                                                                                                                                                                                                                           
            speed: 5.5616218347885614e-5 ns/s                                                                                                                                                                                                                                   
Thread 0x00007f0e1d6bb100 (most recent call first):                                                                                                                                                                                                                             
  File "/data/numerik/people/bzfsikor/conda/envs/conda_jl/lib/python3.13/site-packages/openmm/openmm.py", line 10995 in step                                                                                                                                                    
  File "/data/numerik/people/bzfsikor/conda/envs/conda_jl/lib/python3.13/site-packages/openmm/app/simulation.py", line 229 in _simulate                                                                                                                                         
  File "/data/numerik/people/bzfsikor/conda/envs/conda_jl/lib/python3.13/site-packages/openmm/app/simulation.py", line 150 in step                                                                                                                                              
                                                                                                                                                                                                                                                                                
[29084] signal 6 (-6): Aborted
in expression starting at REPL[2]:1
unknown function (ip: 0x7f0e1d769eec) at /lib/x86_64-linux-gnu/libc.so.6
gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
fatal_error_exit at /usr/local/src/conda/python-3.13.5/Python/pylifecycle.c:3256 [inlined]                                                                                                                                                               |  ETA: 0:03:22
fatal_error at /usr/local/src/conda/python-3.13.5/Python/pylifecycle.c:3402
_Py_FatalErrorFunc at /usr/local/src/conda/python-3.13.5/Python/pylifecycle.c:3488
_Py_EnsureFuncTstateNotNULL at /usr/local/src/conda/python-3.13.5/Include/internal/pycore_pystate.h:189 [inlined]
PyThreadState_Get at /usr/local/src/conda/python-3.13.5/Python/pystate.c:2427 [inlined]

[fabmazz]

My solution (temporary fix I hope) was to launch Julia with `--threads 1,0`, disabling the "interactive" thread which now starts by default with Julia 1.12. This is can be done in IJulia by editing the kernel.json configuration file. I hope a more permanent solution can be devised. Il mar 13 gen 2026, 17:22 Alexander Sikorski ***@***.***> ha scritto:

…

*axsk* left a comment (JuliaPy/PyCall.jl#1095) <#1095 (comment)> Just coming back to Julia after a christmas break, updated to 1.12.4, and was immediately greeted with exactly this as well :( Just for reference, as this might be related: #1090 <#1090> — Reply to this email directly, view it on GitHub <#1095 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADMONLMT7IP3KOWN5QFOGVD4GULU5AVCNFSM6AAAAACQ55OHPGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTONBVGIZTONRQHA> . You are receiving this because you authored the thread.Message ID: ***@***.***>