Segmentation Fault

[axsk]

I keep running into Segmentation fault errors.

This happens most probably during calls to the OpenMM Python API.
Here is my "error message"

[13736] signal 11 (1): Segmentation fault                                                                                                                                                                                                                  
in expression starting at none:0                                                                                                                                                                                                                           
_PyInterpreterState_GET at /usr/local/src/conda/python-3.12.8/Include/internal/pycore_pystate.h:133 [inlined]                                                                                                                                              
get_state at /usr/local/src/conda/python-3.12.8/Objects/obmalloc.c:866 [inlined]                                                                                                                                                                           
_PyObject_Free at /usr/local/src/conda/python-3.12.8/Objects/obmalloc.c:1850 [inlined]
PyObject_Free at /usr/local/src/conda/python-3.12.8/Objects/obmalloc.c:830
_buffer_info_free at /data/numerik/people/bzfsikor/conda/envs/conda_jl/lib/python3.12/site-packages/numpy/core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so (unknown line)
array_dealloc at /data/numerik/people/bzfsikor/conda/envs/conda_jl/lib/python3.12/site-packages/numpy/core/_multiarray_umath.cpython-312-x86_64-linux-gnu.so (unknown line)
pydecref_ at /data/numerik/people/bzfsikor/software/julia_depot/packages/PyCall/1gn3u/src/PyCall.jl:118
pydecref at /data/numerik/people/bzfsikor/software/julia_depot/packages/PyCall/1gn3u/src/PyCall.jl:123
jfptr_pydecref_4550 at /data/numerik/people/bzfsikor/software/julia_depot/compiled/v1.11/PyCall/GkzkC_ddiUX.so (unknown line) 
run_finalizer at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/gc.c:299
jl_gc_run_finalizers_in_list at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/gc.c:389
run_finalizers at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/gc.c:435
enable_finalizers at ./gcutils.jl:161 [inlined]
unlock at ./lock.jl:178 [inlined]
macro expansion at ./lock.jl:275 [inlined]
#282 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:2851
jfptr_YY.282_9263 at /data/numerik/people/bzfsikor/software/julia_depot/compiled/v1.11/REPL/u0gqU_dovaC.so (unknown line)
jl_apply at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
start_task at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/task.c:1202
Allocations: 775171170 (Pool: 775164164; Big: 7006); GC: 5349
fish: Job 1, 'env JULIA_HISTORY=./.history.jl…' terminated by signal SIGSEGV (Address boundary error)

I have no idea how to investigate this further.

[axsk]

And here is another one, which I run into more often. This puzzles me especially since it somehow involves CUDA as well..

in expression starting at REPL[98]:1
_PyInterpreterState_GET at /usr/local/src/conda/python-3.12.8/Include/internal/pycore_pystate.h:133 [inlined]
get_gc_state at /usr/local/src/conda/python-3.12.8/Modules/gcmodule.c:134 [inlined]
PyObject_GC_Del at /usr/local/src/conda/python-3.12.8/Modules/gcmodule.c:2421
pydecref_ at /data/numerik/people/bzfsikor/software/julia_depot/packages/PyCall/1gn3u/src/PyCall.jl:118
pydecref at /data/numerik/people/bzfsikor/software/julia_depot/packages/PyCall/1gn3u/src/PyCall.jl:123
jfptr_pydecref_4550 at /data/numerik/people/bzfsikor/software/julia_depot/compiled/v1.11/PyCall/GkzkC_ddiUX.so (unknown line)
run_finalizer at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/gc.c:299
jl_gc_run_finalizers_in_list at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/gc.c:389
run_finalizers at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/gc.c:435
enable_finalizers at ./gcutils.jl:161 [inlined]
unlock at ./locks-mt.jl:68 [inlined]
popfirst! at ./task.jl:751
trypoptask at ./task.jl:992
jfptr_trypoptask_66779.1 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
get_next_task at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/scheduler.c:377 [inlined]
ijl_task_get_next at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/scheduler.c:438
poptask at ./task.jl:1012
wait at ./task.jl:1021
#wait#731 at ./condition.jl:130
wait at ./condition.jl:125 [inlined]
take! at /data/numerik/people/bzfsikor/software/julia_depot/packages/CUDA/1kIOw/lib/cudadrv/synchronization.jl:53
synchronization_worker at /data/numerik/people/bzfsikor/software/julia_depot/packages/CUDA/1kIOw/lib/cudadrv/synchronization.jl:119
unknown function (ip: 0x7f8cd97c33b5)
jlcapi_synchronization_worker_13623 at /data/numerik/people/bzfsikor/software/julia_depot/compiled/v1.11/CUDA/oWw5k_ddiUX.so (unknown line)
unknown function (ip: 0x7f8f3d3961c3)
unknown function (ip: 0x7f8f3d41685b)
Allocations: 1455439833 (Pool: 1455431030; Big: 8803); GC: 4054
fish: Job 1, 'env JULIA_HISTORY=./.history.jl…' terminated by signal SIGSEGV (Address boundary error)

[axsk]

I switched to a single threaded instance and have not yet observed this issue.
However, I don't make any (explicit) use of multi-threading nowhere in my code..