Open
Description
Affects: PythonCall
Describe the bug
I have installed the ovito library with CondaPkg into a local package I am developing. I can load the package, but the first call to ovito will always crash. In the REPL, I can type ovito and then immediately once I type the . to access some member I get a segfault and the whole terminal freezes. I have tested the python environment this is installed into and the package works fine.
A potential clue: I only get this error when using the System backend. pixi seems to work fine. I have not tried the others.
Edit: Maybe related to #586
Your system
OS: Windows 11
- versioninfo()
Julia Version 1.11.2
Commit 5e9a32e7af (2024-12-01 20:02 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Windows (x86_64-w64-mingw32)
CPU: 16 × 12th Gen Intel(R) Core(TM) i5-12600KF
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, alderlake)
Threads: 6 default, 0 interactive, 3 GC (on 16 virtual cores)
Environment:
JULIA_NUM_THREADS = 6
- Pkg.status():
Project PyVITO v0.0.1
Status `D:\Code\repos\PyVITO\Project.toml`
⌃ [a963bdd2] AtomsBase v0.3.4
[992eb4ea] CondaPkg v0.2.29
⌃ [5789e2e9] FileIO v1.16.1
[ba661fbb] PreferenceTools v0.1.2
[6099a3de] PythonCall v0.9.25
Info Packages marked with ⌃ have new versions available and may be upgradable.
- CondaPkg.status():
CondaPkg Status D:\Code\repos\PyVITO\CondaPkg.toml
Environment
D:\Code\repos\PyVITO\.CondaPkg\env
Packages
ovito v3.12.4 (3.12.4)
Channels
conda-forge
https://conda.ovito.org
Additional context
I have these local preferences set to match the install requirements in the ovito documentation.
channel_order = ["https://conda.ovito.org", "conda-forge"]
channel_priority = "strict"
Error Message:
julia> ovito.
Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x7ffe72126d2d -- PyType_Lookup at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
in expression starting at none:0
PyType_Lookup at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
PyObject_Dir at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
PyObject_Dir at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\C\pointers.jl:303 [inlined]
macro expansion at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\Core\Py.jl:132 [inlined]
pydir at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\Core\builtins.jl:216
propertynames at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\Core\Py.jl:293
unknown function (ip: 000001577fc5ecb2)
complete_symbol at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:208
#complete_identifiers!#57 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:1179
complete_identifiers! at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:1079 [inlined]
completions at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:1436
#complete_line#85 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPL.jl:637
complete_line at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPL.jl:634
jfptr_complete_line_10911.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\share\julia\compiled\v1.11\REPL\u0gqU_hz07T.dll (unknown line)
check_for_hint at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:387
#143 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:2527
jl_apply at C:/workdir/src\julia.h:2157 [inlined]
jl_f__call_latest at C:/workdir/src\builtins.c:875
#invokelatest#2 at .\essentials.jl:1055 [inlined]
invokelatest at .\essentials.jl:1052 [inlined]
#30 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:1711
jfptr_YY.30_8437.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\share\julia\compiled\v1.11\REPL\u0gqU_hz07T.dll (unknown line)
macro expansion at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:2861 [inlined]
macro expansion at .\lock.jl:273 [inlined]
#282 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:2851
jfptr_YY.282_9012.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\share\julia\compiled\v1.11\REPL\u0gqU_hz07T.dll (unknown line)
jl_apply at C:/workdir/src\julia.h:2157 [inlined]
start_task at C:/workdir/src\task.c:1202
Allocations: 7433399 (Pool: 7432925; Big: 474); GC: 14
Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x7ffe722428a4 -- Py_FinalizeEx at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
in expression starting at none:0
Py_FinalizeEx at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
Py_FinalizeEx at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\C\pointers.jl:303 [inlined]
#37 at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\C\context.jl:194
unknown function (ip: 000001577fc5f2f4)
_atexit at .\initdefs.jl:459
jfptr__atexit_71193.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\lib\julia\sys.dll (unknown line)
jl_apply at C:/workdir/src\julia.h:2157 [inlined]
ijl_atexit_hook at C:/workdir/src\init.c:271
ijl_exit at C:/workdir/src\init.c:207
jl_exception_handler at C:/workdir/src\signals-win.c:337 [inlined]
jl_exception_handler at C:/workdir/src\signals-win.c:229
__julia_personality at C:/workdir/src\win32_ucontext.c:28
_chkstk at C:\WINDOWS\SYSTEM32\ntdll.dll (unknown line)
RtlWow64GetCurrentCpuArea at C:\WINDOWS\SYSTEM32\ntdll.dll (unknown line)
KiUserExceptionDispatcher at C:\WINDOWS\SYSTEM32\ntdll.dll (unknown line)
PyType_Lookup at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
PyObject_Dir at D:\Code\repos\PyVITO\.CondaPkg\env\python312.dll (unknown line)
PyObject_Dir at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\C\pointers.jl:303 [inlined]
macro expansion at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\Core\Py.jl:132 [inlined]
pydir at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\Core\builtins.jl:216
propertynames at C:\Users\ejmei\.julia\packages\PythonCall\L4cjh\src\Core\Py.jl:293
unknown function (ip: 000001577fc5ecb2)
complete_symbol at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:208
#complete_identifiers!#57 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:1179
complete_identifiers! at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:1079 [inlined]
completions at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPLCompletions.jl:1436
#complete_line#85 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPL.jl:637
complete_line at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\REPL.jl:634
jfptr_complete_line_10911.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\share\julia\compiled\v1.11\REPL\u0gqU_hz07T.dll (unknown line)
check_for_hint at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:387
#143 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:2527
jl_apply at C:/workdir/src\julia.h:2157 [inlined]
jl_f__call_latest at C:/workdir/src\builtins.c:875
#invokelatest#2 at .\essentials.jl:1055 [inlined]
invokelatest at .\essentials.jl:1052 [inlined]
#30 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:1711
jfptr_YY.30_8437.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\share\julia\compiled\v1.11\REPL\u0gqU_hz07T.dll (unknown line)
macro expansion at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:2861 [inlined]
macro expansion at .\lock.jl:273 [inlined]
#282 at C:\workdir\usr\share\julia\stdlib\v1.11\REPL\src\LineEdit.jl:2851
jfptr_YY.282_9012.1 at C:\Users\ejmei\.julia\juliaup\julia-1.11.2+0.x64.w64.mingw32\share\julia\compiled\v1.11\REPL\u0gqU_hz07T.dll (unknown line)
jl_apply at C:/workdir/src\julia.h:2157 [inlined]
start_task at C:/workdir/src\task.c:1202
Allocations: 7433399 (Pool: 7432925; Big: 474); GC: 14