pytraj segmentation fault with cython 3.0 and cpptraj commit f1d21f688de5ea5c55e650abe6efdbc352bdc613

[hainm]

Version/commit:

cpptraj: Amber-MD/cpptraj@f1d21f6
cython: 3.0.x

How

• Use "-debug" when compiling libcpptraj
• Turn on debug when compiling cython (

  pytraj/setup.py

  Line 126 in 6d62181

  if debug:

  -> if True)

$ cat test.py
import pytraj as pt
pt.load('tz2.pdb')

gdb python3 
run test.py
bt

Get

Thread 1 "python3" received signal SIGABRT, Aborted.
0x0000fffff7d88d78 in raise () from /lib/aarch64-linux-gnu/libc.so.6
(gdb) bt
#0  0x0000fffff7d88d78 in raise () from /lib/aarch64-linux-gnu/libc.so.6
#1  0x0000fffff7d75aac in abort () from /lib/aarch64-linux-gnu/libc.so.6
#2  0x0000fffff7dc2f40 in ?? () from /lib/aarch64-linux-gnu/libc.so.6
#3  0x0000fffff7dca344 in ?? () from /lib/aarch64-linux-gnu/libc.so.6
#4  0x0000fffff7dcbf88 in ?? () from /lib/aarch64-linux-gnu/libc.so.6
#5  0x0000ffffd8ce4a54 in Frame::~Frame() () from /work/cpptraj/lib/libcpptraj.so
#6  0x0000ffffd47653dc in __pyx_pf_6pytraj_10trajectory_5frame_5Frame_2__dealloc__(__pyx_obj_6pytraj_10trajectory_5frame_Frame*) ()
   from /work/pytraj/trajectory/frame.cpython-310-aarch64-linux-gnu.so
#7  0x0000ffffd47650fc in __pyx_pw_6pytraj_10trajectory_5frame_5Frame_3__dealloc__(_object*) () from /work/pytraj/trajectory/frame.cpython-310-aarch64-linux-gnu.so
#8  0x0000ffffd47b4978 in __pyx_tp_dealloc_6pytraj_10trajectory_5frame_Frame(_object*) () from /work/pytraj/trajectory/frame.cpython-310-aarch64-linux-gnu.so
#9  0x0000ffffd42486cc in _Py_DECREF () from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#10 0x0000ffffd4248724 in _Py_XDECREF () from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#11 0x0000ffffd427dc54 in __pyx_pf_6pytraj_10trajectory_6c_traj_12c_trajectory_17TrajectoryCpptraj_33_load_traj_by_indices(__pyx_obj_6pytraj_10trajectory_6c_traj_12c_trajectory_TrajectoryCpptraj*, _object*) () from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#12 0x0000ffffd4277db8 in __pyx_pw_6pytraj_10trajectory_6c_traj_12c_trajectory_17TrajectoryCpptraj_34_load_traj_by_indices(_object*, _object* const*, long, _object*) ()
   from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#13 0x0000ffffd42b060c in __Pyx_CyFunction_Vectorcall_FASTCALL_KEYWORDS(_object*, _object* const*, unsigned long, _object*) ()
   from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#14 0x0000ffffd42a8268 in __Pyx_PyObject_FastCallDict(_object*, _object**, unsigned long, _object*) ()
   from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#15 0x0000ffffd4270238 in __pyx_pf_6pytraj_10trajectory_6c_traj_12c_trajectory_17TrajectoryCpptraj_25__getitem__(__pyx_obj_6pytraj_10trajectory_6c_traj_12c_trajectory_TrajectoryCpptraj*, _object*) () from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#16 0x0000ffffd426d2b8 in __pyx_pw_6pytraj_10trajectory_6c_traj_12c_trajectory_17TrajectoryCpptraj_26__getitem__(_object*, _object*) ()
   from /work/pytraj/trajectory/c_traj/c_trajectory.cpython-310-aarch64-linux-gnu.so
#17 0x0000aaaaaab08bb4 in _PyEval_EvalFrameDefault ()
#18 0x0000aaaaaabb7450 in _PyEval_Vector ()
#19 0x0000aaaaaab0c1c0 in _PyEval_EvalFrameDefault ()
#20 0x0000aaaaaabb7450 in _PyEval_Vector ()
#21 0x0000aaaaaabb7644 in PyEval_EvalCode ()
#22 0x0000aaaaaabf6bac in run_eval_code_obj ()
#23 0x0000aaaaaabf6e48 in run_mod ()
#24 0x0000aaaaaabf6f68 in pyrun_file ()
#25 0x0000aaaaaabf95a4 in _PyRun_SimpleFileObject ()
#26 0x0000aaaaaabf9be0 in _PyRun_AnyFileObject ()
#27 0x0000aaaaaab0f888 in Py_RunMain ()
#28 0x0000aaaaaab0fec4 in Py_BytesMain ()
#29 0x0000fffff7d75e10 in __libc_start_main () from /lib/aarch64-linux-gnu/libc.so.6
#30 0x0000aaaaaab0e6b8 in _start ()
Backtrace stopped: previous frame identical to this frame (corrupt stack?)

[hainm]

Remove this line

pytraj/pytraj/trajectory/frame.pyx

Line 140 in 6d62181

del self.thisptr

will help pt.load('tz2.pdb') run fine.