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Crazy segmentation fault (core dumped) for openmm simulation

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Crazy segmentation fault (core dumped) for openmm simulation

Posted: Tue Oct 01, 2024 2:39 pm
by ningw2
Hi there,

I'm using openmm running simulations for a transporter project with 155717 atoms. I keep getting "/home/ning/openmm/lib/python3.11/site-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to <class 'numpy.float32'>
warnings.warn(
Segmentation fault (core dumped)" error. The issue occurs during different simulation times (sometimes 30%, 60%, and 94%), and it will happen for both OpenMM Version: 7.6 and OpenMM Version: 8.1.2.

Any suggestions?

Thanks in advance.

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Wed Oct 02, 2024 7:32 am
by peastman
The error message says it's happening in mdtraj/utils/validation.py. That's part of MDTraj, not OpenMM.

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Wed Oct 02, 2024 7:44 am
by ningw2
Hi Peter, thanks for reply. The thing is that mdtraj/utils/validation.py is the one caused the warning. Warning will show up every time but it's not the reason caused segmentation fault. Any other idea on fixing this?

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Wed Oct 02, 2024 7:51 am
by peastman
The first step is to find out where the segfault is happening. You can do that by running your script inside gdb. Type "gdb python" from the console, then at the gdb prompt "run myscript.py", except using the actual name of your script and including any command line options. It will run until the segfault happens. At that point you'll return to the gdb prompt. Type "bt" to get a trace of where it happened. Post the complete output of that command here.

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Wed Oct 02, 2024 11:10 am
by ningw2
Here's the bt results:

Code: Select all

(gdb) bt
#0  0x0000000000000000 in ?? ()
#1  0x000055555567ad5e in _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x555572829090, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3308
#2  0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x555572829090, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#3  function_code_fastcall (tstate=0x5555558fa500, co=0x7fff4f9ba9d0, args=<optimized out>, nargs=3, globals=0x7fff4f987040) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#4  0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55558c383718, callable=0x7fff4f943ca0, tstate=0x5555558fa500)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#5  PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55558c383718, callable=0x7fff4f943ca0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#6  call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#7  _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55558c383550, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#8  0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x55558c383550, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#9  function_code_fastcall (tstate=0x5555558fa500, co=0x7fffb719da80, args=<optimized out>, nargs=3, globals=0x7fffb717b5c0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#10 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55558c28c360, callable=0x7fffb70d3e50, tstate=0x5555558fa500)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#11 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55558c28c360, callable=0x7fffb70d3e50) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#12 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#13 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55558c28c180, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#14 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x55558c28c180, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#15 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x7fffc85d4fb8, kwargs=0x7ffe8158fd90, 
    kwcount=<optimized out>, kwstep=1, defs=0x7fffb70d45d8, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7fffb71a8d30, qualname=0x7fffb714e440) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#16 0x0000555555697f5b in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7ffe8158fd88, func=0x7fffb70d3dc0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#17 _PyObject_VectorcallTstate (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7ffe8158fd88, callable=0x7fffb70d3dc0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#18 method_vectorcall (method=<optimized out>, args=0x7ffe8158fd90, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/classobject.c:53
#19 0x000055555567b5c7 in _PyObject_VectorcallTstate (kwnames=0x7fffc85d4fa0, nargsf=<optimized out>, args=<optimized out>, callable=0x7ffe7edcbdc0, tstate=0x5555558fa500)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#20 PyObject_Vectorcall (kwnames=0x7fffc85d4fa0, nargsf=<optimized out>, args=<optimized out>, callable=0x7ffe7edcbdc0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#21 call_function (kwnames=0x7fffc85d4fa0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#22 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffe8158fc10, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3537
#23 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x7ffe8158fc10, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#24 function_code_fastcall (tstate=0x5555558fa500, co=0x7fffb719d660, args=<optimized out>, nargs=2, globals=0x7fffb717b5c0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#25 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x555555956500, callable=0x7fffb70d3ca0, tstate=0x5555558fa500)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#26 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x555555956500, callable=0x7fffb70d3ca0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#27 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#28 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x555555956390, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#29 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x555555956390, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#30 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x0, kwcount=<optimized out>, kwstep=2, 
    defs=0x0, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#31 0x00005555556792c8 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x0, kwcount=0, 
    kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4361
#32 0x0000555555679279 in PyEval_EvalCodeEx (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kws=<optimized out>, kwcount=0, defs=0x0, defcount=0, 
    kwdefs=0x0, closure=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4377
#33 0x00005555557244fb in PyEval_EvalCode (co=co@entry=0x7ffff7bbd9d0, globals=globals@entry=0x7ffff7bb4680, locals=locals@entry=0x7ffff7bb4680) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:828
#34 0x000055555575188a in run_eval_code_obj (tstate=0x5555558fa500, co=0x7ffff7bbd9d0, globals=0x7ffff7bb4680, locals=0x7ffff7bb4680) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1221
#35 0x000055555574dd33 in run_mod (mod=<optimized out>, filename=<optimized out>, globals=0x7ffff7bb4680, locals=0x7ffff7bb4680, flags=<optimized out>, arena=<optimized out>)
    at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1242
#36 0x00005555555e85c7 in pyrun_file (fp=0x5555558f7850, filename=0x7ffff7562430, start=<optimized out>, globals=0x7ffff7bb4680, locals=0x7ffff7bb4680, closeit=1, flags=0x7fffffffdb88)
    at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1140
#37 0x0000555555747c50 in pyrun_simple_file (flags=0x7fffffffdb88, closeit=1, filename=0x7ffff7562430, fp=0x5555558f7850) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:450
#38 PyRun_SimpleFileExFlags (fp=0x5555558f7850, filename=<optimized out>, closeit=1, flags=0x7fffffffdb88) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:483
#39 0x0000555555745284 in pymain_run_file (cf=0x7fffffffdb88, config=0x5555558f8b30) at /usr/local/src/conda/python-3.9.20/Modules/main.c:377
#40 pymain_run_python (exitcode=0x7fffffffdb80) at /usr/local/src/conda/python-3.9.20/Modules/main.c:606
--Type <RET> for more, q to quit, c to continue without paging--c
#41 Py_RunMain () at /usr/local/src/conda/python-3.9.20/Modules/main.c:685
#42 0x0000555555718327 in Py_BytesMain (argc=<optimized out>, argv=<optimized out>) at /usr/local/src/conda/python-3.9.20/Modules/main.c:1105
#43 0x00007ffff7c29d90 in __libc_start_call_main (main=main@entry=0x5555557182e0 <main>, argc=argc@entry=2, argv=argv@entry=0x7fffffffddb8) at ../sysdeps/nptl/libc_start_call_main.h:58
#44 0x00007ffff7c29e40 in __libc_start_main_impl (main=0x5555557182e0 <main>, argc=2, argv=0x7fffffffddb8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdda8) at ../csu/libc-start.c:392
#45 0x000055555571823e in _start ()

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Wed Oct 02, 2024 1:54 pm
by ningw2
peastman wrote: ↑
Wed Oct 02, 2024 7:51 am
 The first step is to find out where the segfault is happening. You can do that by running your script inside gdb. Type "gdb python" from the console, then at the gdb prompt "run myscript.py", except using the actual name of your script and including any command line options. It will run until the segfault happens. At that point you'll return to the gdb prompt. Type "bt" to get a trace of where it happened. Post the complete output of that command here.
I ran again and got output below.

Code: Select all

/home/ning/miniconda3/envs/omm7.6/lib/python3.9/site-packages/mdtraj/utils/validation.py:123: TypeCastPerformanceWarning: Casting xyz dtype=float64 to <class 'numpy.float32'> 
  warnings.warn(
double free or corruption (!prev)

Thread 1 "python" received signal SIGABRT, Aborted.
__pthread_kill_implementation (no_tid=0, signo=6, threadid=140737352738624) at ./nptl/pthread_kill.c:44
44	./nptl/pthread_kill.c: No such file or directory.
(gdb) bt
#0  __pthread_kill_implementation (no_tid=0, signo=6, threadid=140737352738624) at ./nptl/pthread_kill.c:44
#1  __pthread_kill_internal (signo=6, threadid=140737352738624) at ./nptl/pthread_kill.c:78
#2  __GI___pthread_kill (threadid=140737352738624, signo=signo@entry=6) at ./nptl/pthread_kill.c:89
#3  0x00007ffff7c42476 in __GI_raise (sig=sig@entry=6) at ../sysdeps/posix/raise.c:26
#4  0x00007ffff7c287f3 in __GI_abort () at ./stdlib/abort.c:79
#5  0x00007ffff7c89676 in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff7ddbb77 "%s\n") at ../sysdeps/posix/libc_fatal.c:155
#6  0x00007ffff7ca0cfc in malloc_printerr (str=str@entry=0x7ffff7dde7b0 "double free or corruption (!prev)") at ./malloc/malloc.c:5664
#7  0x00007ffff7ca2e7c in _int_free (av=0x7ffff7e1ac80 <main_arena>, p=0x55558836e600, have_lock=<optimized out>) at ./malloc/malloc.c:4591
#8  0x00007ffff7ca5453 in __GI___libc_free (mem=<optimized out>) at ./malloc/malloc.c:3391
#9  0x000055555566dd2f in _PyMem_RawFree (ptr=<optimized out>, ctx=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/obmalloc.c:127
#10 PyMem_RawFree (ptr=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/obmalloc.c:595
#11 _PyObject_Free (ctx=<optimized out>, p=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/obmalloc.c:1922
#12 _PyObject_Free (p=<optimized out>, ctx=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/obmalloc.c:1913
#13 PyMem_Free (ptr=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/obmalloc.c:629
#14 list_dealloc (op=0x7ffeabfb9080) at /usr/local/src/conda/python-3.9.20/Objects/listobject.c:345
#15 0x00005555555bbe7f in _Py_DECREF (op=<optimized out>) at /usr/local/src/conda/python-3.9.20/Include/object.h:430
#16 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x5555727505d0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:1992
#17 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x5555727505d0, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#18 function_code_fastcall (tstate=0x5555558fa2c0, co=0x7fff479bba80, args=<optimized out>, nargs=3, globals=0x7fff479b5c40) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#19 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55558c3f74a8, callable=0x7fff47947ca0, tstate=0x5555558fa2c0)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#20 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55558c3f74a8, callable=0x7fff47947ca0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#21 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#22 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55558c3f72e0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#23 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x55558c3f72e0, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#24 function_code_fastcall (tstate=0x5555558fa2c0, co=0x7fffb71a1b30, args=<optimized out>, nargs=3, globals=0x7fffb7180180) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#25 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55557d038920, callable=0x7fffb70d7e50, tstate=0x5555558fa2c0)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#26 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55557d038920, callable=0x7fffb70d7e50) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#27 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#28 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55557d038740, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#29 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x55557d038740, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#30 _PyEval_EvalCode (tstate=0x5555558fa2c0, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x7fffd0e79088, kwargs=0x7ffe81451d90, 
    kwcount=<optimized out>, kwstep=1, defs=0x7fffb70ca218, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7fffb71ab8f0, qualname=0x7fffb71506c0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#31 0x0000555555697f5b in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7ffe81451d88, func=0x7fffb70d7dc0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#32 _PyObject_VectorcallTstate (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7ffe81451d88, callable=0x7fffb70d7dc0, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#33 method_vectorcall (method=<optimized out>, args=0x7ffe81451d90, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/classobject.c:53
#34 0x000055555567b5c7 in _PyObject_VectorcallTstate (kwnames=0x7fffd0e79070, nargsf=<optimized out>, args=<optimized out>, callable=0x7ffe7f112d40, tstate=0x5555558fa2c0)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#35 PyObject_Vectorcall (kwnames=0x7fffd0e79070, nargsf=<optimized out>, args=<optimized out>, callable=0x7ffe7f112d40) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#36 call_function (kwnames=0x7fffd0e79070, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#37 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffe81451c10, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3537
#38 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x7ffe81451c10, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#39 function_code_fastcall (tstate=0x5555558fa2c0, co=0x7fffb71a1710, args=<optimized out>, nargs=2, globals=0x7fffb7180180) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#40 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x5555559571c0, callable=0x7fffb70d7ca0, tstate=0x5555558fa2c0)
    at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#41 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x5555559571c0, callable=0x7fffb70d7ca0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#42 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#43 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x555555957050, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#44 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x555555957050, tstate=0x5555558fa2c0) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#45 _PyEval_EvalCode (tstate=0x5555558fa2c0, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x0, kwcount=<optimized out>, kwstep=2, 
--Type <RET> for more, q to quit, c to continue without paging--RET
    defs=0x0, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#46 0x00005555556792c8 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x0, kwcount=0, 
    kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4361
#47 0x0000555555679279 in PyEval_EvalCodeEx (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kws=<optimized out>, kwcount=0, defs=0x0, defcount=0, 
    kwdefs=0x0, closure=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4377
#48 0x00005555557244fb in PyEval_EvalCode (co=co@entry=0x7ffff7bbea80, globals=globals@entry=0x7ffff7bb9180, locals=locals@entry=0x7ffff7bb9180) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:828
#49 0x000055555575188a in run_eval_code_obj (tstate=0x5555558fa2c0, co=0x7ffff7bbea80, globals=0x7ffff7bb9180, locals=0x7ffff7bb9180) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1221
#50 0x000055555574dd33 in run_mod (mod=<optimized out>, filename=<optimized out>, globals=0x7ffff7bb9180, locals=0x7ffff7bb9180, flags=<optimized out>, arena=<optimized out>)
    at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1242
#51 0x00005555555e85c7 in pyrun_file (fp=0x5555558f7690, filename=0x7ffff7e51490, start=<optimized out>, globals=0x7ffff7bb9180, locals=0x7ffff7bb9180, closeit=1, flags=0x7fffffffc448)
    at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1140
#52 0x0000555555747c50 in pyrun_simple_file (flags=0x7fffffffc448, closeit=1, filename=0x7ffff7e51490, fp=0x5555558f7690) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:450
#53 PyRun_SimpleFileExFlags (fp=0x5555558f7690, filename=<optimized out>, closeit=1, flags=0x7fffffffc448) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:483
#54 0x0000555555745284 in pymain_run_file (cf=0x7fffffffc448, config=0x5555558f8970) at /usr/local/src/conda/python-3.9.20/Modules/main.c:377
#55 pymain_run_python (exitcode=0x7fffffffc440) at /usr/local/src/conda/python-3.9.20/Modules/main.c:606
#56 Py_RunMain () at /usr/local/src/conda/python-3.9.20/Modules/main.c:685
#57 0x0000555555718327 in Py_BytesMain (argc=<optimized out>, argv=<optimized out>) at /usr/local/src/conda/python-3.9.20/Modules/main.c:1105
#58 0x00007ffff7c29d90 in __libc_start_call_main (main=main@entry=0x5555557182e0 <main>, argc=argc@entry=2, argv=argv@entry=0x7fffffffc678) at ../sysdeps/nptl/libc_start_call_main.h:58
#59 0x00007ffff7c29e40 in __libc_start_main_impl (main=0x5555557182e0 <main>, argc=2, argv=0x7fffffffc678, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffc668)
    at ../csu/libc-start.c:392
#60 0x000055555571823e in _start ()
(gdb)

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Thu Oct 03, 2024 10:55 am
by peastman
What model of CPU are you using? The exact part number, not just a generic term like "i7".

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Thu Oct 03, 2024 11:33 am
by ningw2
The model name is Intel(R) Core(TM) i9-14900KF

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Thu Oct 03, 2024 11:48 am
by peastman
That's what I guessed. Your CPU is affected by a bug that causes it to use voltages that are too high, leading to overheating and instability. See Intel's writeup of the problem for details. They've released a set of microcode updates that fix the problem. You should be able to get them from the computer or motherboard's manufacturer.

Fixing this is very important, because the overheating can also cause permanent damage to the CPU.

Re: Crazy segmentation fault (core dumped) for openmm simulation

Posted: Fri Oct 25, 2024 8:38 am
by ningw2
Hi Peter,

I updated my BIOs according to your instruction, but I still get segmentation fault. Below is the result from "bt" command. Could you please take a look and let me know how to fix it? Thanks!!!

Code: Select all

Thread 1 "python" received signal SIGSEGV, Segmentation fault.
0x00007ffe65acbf70 in ?? ()
(gdb) bt
#0  0x00007ffe65acbf70 in ?? ()
#1  0x0000555555698c3b in PyObject_Hash (v=0x7ffe65acc350) at /usr/local/src/conda/python-3.9.20/Objects/object.c:769
#2  dict_get_impl (default_value=0x5555558c6d60 <_Py_NoneStruct>, key=0x7ffe65acc350, self=0x7fffd9996e80) at /usr/local/src/conda/python-3.9.20/Objects/dictobject.c:2903
#3  dict_get (nargs=<optimized out>, args=<optimized out>, self=0x7fffd9996e80) at /usr/local/src/conda/python-3.9.20/Objects/clinic/dictobject.c.h:76
#4  method_vectorcall_FASTCALL (func=<optimized out>, args=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/descrobject.c:390
#5  0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7ffe53c9cd98, callable=0x7ffff7e820e0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#6  PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7ffe53c9cd98, callable=0x7ffff7e820e0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#7  call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#8  _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffe53c9cbe0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#9  0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x7ffe53c9cbe0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#10 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x555555b53c80, kwcount=<optimized out>, kwstep=1, 
    defs=0x7ffff72f5898, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7ffff73a4a70, qualname=0x7ffff73a4a70) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#11 0x000055555568ab89 in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#12 0x000055555567a80f in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x555555b53c70, callable=0x7fffd0f5bd30, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#13 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x555555b53c70, callable=0x7fffd0f5bd30) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#14 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#15 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x555555b53ac0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3520
#16 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x555555b53ac0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#17 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x7ffe7ea2eda8, kwcount=<optimized out>, kwstep=1, 
    defs=0x7ffff7339988, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7ffff72f5b30, qualname=0x7ffff72f5b30) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#18 0x000055555568ab89 in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#19 0x000055555567a80f in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7ffe7ea2ed98, callable=0x7fffd0f5be50, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#20 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7ffe7ea2ed98, callable=0x7fffd0f5be50) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#21 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#22 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffe7ea2ebe0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3520
#23 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x7ffe7ea2ebe0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#24 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x7fffd0e56210, kwcount=<optimized out>, kwstep=1, 
    defs=0x7ffff72f5898, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7ffff73a4a70, qualname=0x7ffff73a4a70) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#25 0x000055555568ab89 in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#26 0x000055555567ed9e in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7fffd0e56208, callable=0x7fffd0f5bd30, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#27 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffd0e56208, callable=0x7fffd0f5bd30) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#28 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#29 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7fffd0e56040, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3489
#30 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x7fffd0e56040, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#31 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x7ffff74861e0, kwcount=<optimized out>, kwstep=1, 
    defs=0x7fffd0f07208, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7fffd0f003a0, qualname=0x7fffd0f72c30) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#32 0x0000555555697f5b in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7ffff74861c8, func=0x7fffd0f0ac10) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#33 _PyObject_VectorcallTstate (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7ffff74861c8, callable=0x7fffd0f0ac10, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#34 method_vectorcall (method=<optimized out>, args=0x7ffff74861d0, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/classobject.c:53
#35 0x000055555567ed9e in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7ffff74861d0, callable=0x7ffe7eabe4c0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#36 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7ffff74861d0, callable=0x7ffe7eabe4c0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#37 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#38 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffff7486040, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3489
#39 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x7ffff7486040, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#40 function_code_fastcall (tstate=0x5555558fa500, co=0x7fffd0f05030, args=<optimized out>, nargs=2, globals=0x7fffd0f618c0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#41 0x0000555555697eae in _PyFunction_Vectorcall (kwnames=0x0, nargsf=<optimized out>, stack=0x7ffff73aaa38, func=0x7fffd0f0ab80) at /usr/local/src/conda/python-3.9.20/Objects/call.c:367
#42 _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7ffff73aaa38, callable=0x7fffd0f0ab80, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#43 method_vectorcall (method=<optimized out>, args=0x7ffff73aaa40, nargsf=<optimized out>, kwnames=0x0) at /usr/local/src/conda/python-3.9.20/Objects/classobject.c:53
#44 0x000055555567ed9e in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7ffff73aaa40, callable=0x7ffe7eabe900, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#45 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7ffff73aaa40, callable=0x7ffe7eabe900) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#46 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#47 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffff73aa8b0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3489
#48 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x7ffff73aa8b0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#49 function_code_fastcall (tstate=0x5555558fa500, co=0x7fffd0f01df0, args=<optimized out>, nargs=2, globals=0x7fffd0f618c0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#50 0x0000555555697eae in _PyFunction_Vectorcall (kwnames=0x0, nargsf=<optimized out>, stack=0x55558c26c478, func=0x7fffd0f0a9d0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:367
#51 _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55558c26c478, callable=0x7fffd0f0a9d0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#52 method_vectorcall (method=<optimized out>, args=0x55558c26c480, nargsf=<optimized out>, kwnames=0x0) at /usr/local/src/conda/python-3.9.20/Objects/classobject.c:53
#53 0x000055555567ed9e in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55558c26c480, callable=0x7ffe7eabe340, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#54 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55558c26c480, callable=0x7ffe7eabe340) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#55 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#56 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55558c26c2a0, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3489
#57 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x55558c26c2a0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#58 function_code_fastcall (tstate=0x5555558fa500, co=0x7fff4f9b99d0, args=<optimized out>, nargs=3, globals=0x7fff4f987340) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
--Type <RET> for more, q to quit, c to continue without paging--c
#59 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55558c1c1c28, callable=0x7fff4f945ca0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#60 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55558c1c1c28, callable=0x7fff4f945ca0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#61 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#62 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55558c1c1a60, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#63 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x55558c1c1a60, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#64 function_code_fastcall (tstate=0x5555558fa500, co=0x7fffb719fa80, args=<optimized out>, nargs=3, globals=0x7fffb717b780) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#65 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x55559b68dd60, callable=0x7fffb70d5e50, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#66 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x55559b68dd60, callable=0x7fffb70d5e50) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#67 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#68 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x55559b68db80, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#69 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x55559b68db80, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#70 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x7fffc85d4fe8, kwargs=0x7ffe7ea31d90, kwcount=<optimized out>, kwstep=1, defs=0x7fffb70d4858, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x7fffb71a8ef0, qualname=0x7fffb7152210) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#71 0x0000555555697f5b in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7ffe7ea31d88, func=0x7fffb70d5dc0) at /usr/local/src/conda/python-3.9.20/Objects/call.c:396
#72 _PyObject_VectorcallTstate (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7ffe7ea31d88, callable=0x7fffb70d5dc0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#73 method_vectorcall (method=<optimized out>, args=0x7ffe7ea31d90, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/local/src/conda/python-3.9.20/Objects/classobject.c:53
#74 0x000055555567b5c7 in _PyObject_VectorcallTstate (kwnames=0x7fffc85d4fd0, nargsf=<optimized out>, args=<optimized out>, callable=0x7ffe7eabefc0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#75 PyObject_Vectorcall (kwnames=0x7fffc85d4fd0, nargsf=<optimized out>, args=<optimized out>, callable=0x7ffe7eabefc0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#76 call_function (kwnames=0x7fffc85d4fd0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#77 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x7ffe7ea31c10, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3537
#78 0x000055555568ae2a in _PyEval_EvalFrame (throwflag=0, f=0x7ffe7ea31c10, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#79 function_code_fastcall (tstate=0x5555558fa500, co=0x7fffb719f660, args=<optimized out>, nargs=2, globals=0x7fffb717b780) at /usr/local/src/conda/python-3.9.20/Objects/call.c:330
#80 0x000055555567aac4 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x555555956500, callable=0x7fffb70d5ca0, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:118
#81 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x555555956500, callable=0x7fffb70d5ca0) at /usr/local/src/conda/python-3.9.20/Include/cpython/abstract.h:127
#82 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:5077
#83 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=0x555555956390, throwflag=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:3506
#84 0x0000555555679615 in _PyEval_EvalFrame (throwflag=0, f=0x555555956390, tstate=0x5555558fa500) at /usr/local/src/conda/python-3.9.20/Include/internal/pycore_ceval.h:40
#85 _PyEval_EvalCode (tstate=0x5555558fa500, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=0x0, kwargs=0x0, kwcount=<optimized out>, kwstep=2, defs=0x0, defcount=<optimized out>, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4329
#86 0x00005555556792c8 in _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x0, kwcount=0, kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4361
#87 0x0000555555679279 in PyEval_EvalCodeEx (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kws=<optimized out>, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:4377
#88 0x00005555557244fb in PyEval_EvalCode (co=co@entry=0x7ffff7bbd9d0, globals=globals@entry=0x7ffff7bb36c0, locals=locals@entry=0x7ffff7bb36c0) at /usr/local/src/conda/python-3.9.20/Python/ceval.c:828
#89 0x000055555575188a in run_eval_code_obj (tstate=0x5555558fa500, co=0x7ffff7bbd9d0, globals=0x7ffff7bb36c0, locals=0x7ffff7bb36c0) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1221
#90 0x000055555574dd33 in run_mod (mod=<optimized out>, filename=<optimized out>, globals=0x7ffff7bb36c0, locals=0x7ffff7bb36c0, flags=<optimized out>, arena=<optimized out>) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1242
#91 0x00005555555e85c7 in pyrun_file (fp=0x5555558f7850, filename=0x7ffff7563430, start=<optimized out>, globals=0x7ffff7bb36c0, locals=0x7ffff7bb36c0, closeit=1, flags=0x7fffffffda98) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:1140
#92 0x0000555555747c50 in pyrun_simple_file (flags=0x7fffffffda98, closeit=1, filename=0x7ffff7563430, fp=0x5555558f7850) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:450
#93 PyRun_SimpleFileExFlags (fp=0x5555558f7850, filename=<optimized out>, closeit=1, flags=0x7fffffffda98) at /usr/local/src/conda/python-3.9.20/Python/pythonrun.c:483
#94 0x0000555555745284 in pymain_run_file (cf=0x7fffffffda98, config=0x5555558f8b30) at /usr/local/src/conda/python-3.9.20/Modules/main.c:377
#95 pymain_run_python (exitcode=0x7fffffffda90) at /usr/local/src/conda/python-3.9.20/Modules/main.c:606
#96 Py_RunMain () at /usr/local/src/conda/python-3.9.20/Modules/main.c:685
#97 0x0000555555718327 in Py_BytesMain (argc=<optimized out>, argv=<optimized out>) at /usr/local/src/conda/python-3.9.20/Modules/main.c:1105
#98 0x00007ffff7c29d90 in __libc_start_call_main (main=main@entry=0x5555557182e0 <main>, argc=argc@entry=2, argv=argv@entry=0x7fffffffdcc8) at ../sysdeps/nptl/libc_start_call_main.h:58
#99 0x00007ffff7c29e40 in __libc_start_main_impl (main=0x5555557182e0 <main>, argc=2, argv=0x7fffffffdcc8, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdcb8) at ../csu/libc-start.c:392
#100 0x000055555571823e in _start ()
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