Segmentation Fault #1090
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And here is another one, which I run into more often. This puzzles me especially since it somehow involves CUDA as well.. Stacktrace[89762] signal 11 (1): Segmentation fault
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) |
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I switched to a single threaded instance and have not yet observed this issue. |
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Whereas above examples happened randomly in my training loop, I can now reproduce the problem by tab-completing a PyObjets fields: Stacktracejulia> a[1]
PyObject <Atom 0 (H1) of chain 0 residue 0 (ACE)>
julia> a[1].
[12951] 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]
_PyType_Lookup at /usr/local/src/conda/python-3.12.8/Objects/typeobject.c:4729 [inlined]
_PyObject_LookupSpecial at /usr/local/src/conda/python-3.12.8/Objects/typeobject.c:2167
_dir_object at /usr/local/src/conda/python-3.12.8/Objects/object.c:1758 [inlined]
PyObject_Dir at /usr/local/src/conda/python-3.12.8/Objects/object.c:1790
macro expansion at /data/numerik/people/bzfsikor/software/julia_depot/packages/PyCall/1gn3u/src/exception.jl:108 [inlined]
propertynames at /data/numerik/people/bzfsikor/software/julia_depot/packages/PyCall/1gn3u/src/PyCall.jl:327
propertynames at ./reflection.jl:2612
unknown function (ip: 0x7f671ed24e4b)
complete_symbol at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/REPLCompletions.jl:208
#complete_identifiers!#57 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/REPLCompletions.jl:1179
complete_identifiers! at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/REPLCompletions.jl:1079 [inlined]
completions at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/REPLCompletions.jl:1436
#complete_line#85 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/REPL.jl:637
complete_line at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/REPL.jl:634
unknown function (ip: 0x7f68d8d8d97d)
check_for_hint at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:387
#143 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:2527
jl_apply at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1055 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
#30 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:1711
jfptr_YY.30_8684 at /data/numerik/people/bzfsikor/software/julia_depot/compiled/v1.11/REPL/u0gqU_dovaC.so (unknown line)
#254 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:2614
jl_apply at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/builder-demeter6-3/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1055 [inlined]
invokelatest at ./essentials.jl:1052 [inlined]
#30 at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:1711
jfptr_YY.30_8724 at /data/numerik/people/bzfsikor/software/julia_depot/compiled/v1.11/REPL/u0gqU_dovaC.so (unknown line)
macro expansion at /home/htc/bzfsikor/.julia/juliaup/julia-1.11.3+0.x64.linux.gnu/share/julia/stdlib/v1.11/REPL/src/LineEdit.jl:2861 [inlined]
macro expansion at ./lock.jl:273 [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: 66606445 (Pool: 66604355; Big: 2090); GC: 104
fish: Job 1, 'env JULIA_HISTORY=./.history.jl…' terminated by signal SIGSEGV (Address boundary error)Again, this only happens with multiple threads, when starting Julia with |
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Here's a simple script that reliably triggers a similar segfault for me: using PyCall
const math = pyimport("math")
println("nthreads = ", Threads.nthreads())
function foo(n, niter=1)
x = zeros(n)
for iter = 1:niter
Threads.@threads for i = 1:n
x[i] += rand()
end
end
return x
end
foo(50_000, 25_000)Output on Linux with Julia 1.11.4 and Python 3.12.9Output on macos with Julia 1.11.3 and Python 3.13.2On my mac this crashes about 90% of the time. If I comment out the |
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Using the |
This was referenced Apr 14, 2025
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I keep running into
Segmentation faulterrors.This happens most probably during calls to the OpenMM Python API.
Here is my "error message"
Stacktrace
I have no idea how to investigate this further.
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