Heisenbug that kills process via SIGALRM

Bug report

Bug description:

First of all, I know exactly how this bug is going to sound: batshit insane. I implore you to keep reading.

I've had a timer application for ages that uses signal.alarm() concurrently with input() so that it has a rudimentary way of displaying things in the background while still allowing user interaction on the CLI. The gist of it is this:

@staticmethod
def _input_timeout(prompt, timeout_secs):
	class TimeExpiredException(Exception): pass

	def raise_exception(signum, frame):
		raise TimeExpiredException()

	signal.signal(signal.SIGALRM, raise_exception)
	try:
		signal.alarm(timeout_secs)
		result = input(prompt)
		signal.alarm(0)
	except TimeExpiredException:
		result = None
	return result

This program has mysteriously stopped working with Python 3.13.3 with an exceptionally strange error mode: my signal handler is called from somewhere I apparently do not expect (HelpFormatter), causing the whole process to terminate. This always happens after exactly 29 seconds when I run my process as user and after exactly 25 seconds when I run as root. It happens only when there is no __pycache__ present, i.e., when the Python bytecode is generated on startup.

I tried creating a minimal reproducer, which was super difficult. Even when I remove dead code from the Python script, the bug stops triggering. Some code removal was fine, but for example if I remove the wrapper around argparse, the bug disappears.

As I said. This sounds batshit crazy.

When the mystery signal is caught, it gives one final indication where it comes from:

reliant [/tmp/heisenbug]: rm -fr __pycache__/ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m25,035s
user	0m0,025s
sys	0m0,011s

Note the message: Exception ignored in tp_clear of HelpFormatter: (this was running as root, you see that it took 25 seconds.)

Just so you believe me that it always triggers after the same time, here are three consecutive runs as root (I swear this is not copy paste, timings are accurate to millisecond level!):

reliant [/tmp/heisenbug]: rm -fr __pycache__/ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m25,035s
user	0m0,025s
sys	0m0,011s

reliant [/tmp/heisenbug]: rm -fr __pycache__/ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m25,035s
user	0m0,025s
sys	0m0,011s

reliant [/tmp/heisenbug]: rm -fr __pycache__/ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m25,035s
user	0m0,025s
sys	0m0,010s

And here some runs as user:

reliant joe [/tmp/heisenbug]: rm -fr __pycache__ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m29,038s
user	0m0,029s
sys	0m0,010s

reliant joe [/tmp/heisenbug]: rm -fr __pycache__ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m29,039s
user	0m0,027s
sys	0m0,012s

reliant joe [/tmp/heisenbug]: rm -fr __pycache__ && time ./stopwatch 
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 Exception ignored in tp_clear of HelpFormatter:
Traceback (most recent call last):
  File "/tmp/heisenbug/./stopwatch", line 69, in raise_exception
    raise TimeExpiredException()
StopWatch._input_timeout.<locals>.TimeExpiredException: 
FINALLY

real	0m29,038s
user	0m0,029s
sys	0m0,009s

I'm running on 6.14.0-15-generic #15-Ubuntu. My CPU is an AMD Ryzen Threadripper PRO 3945WX 12-Cores. I'm using the Ubuntu-provided Python package (Ubuntu calls it 3.13.3-1):

Python 3.13.3 (main, Apr  8 2025, 19:55:40) [GCC 14.2.0] on linux

I cannot reproduce this issue on Debian with Python 3.11/ARM nor on another Ubuntu with Python 3.12/x86_64.

I cannot attach files (the reproducer) to this bug, so here it is as base64:

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You can simply unpack it by doing:

$ openssl base64 -d | tar xvz

And pasting the above base64 blob in. Remember you have to clear __pycache__ to trigger the bug. I'm including the bytecode in case it contains something interesting.

Please someone tell me this is reproducible and I'm not completely losing my marbles.

CPython versions tested on:

3.13

Operating systems tested on:

Linux

首先解包提供的 base64 reproducer，清除 pycache，并在 Linux 上使用 Python 3.13.3 运行 ./stopwatch。将其行为与 Python 3.11 和 3.12 进行比较，然后缩小 signal.alarm()、input()、argparse、字节码生成和 HelpFormatter 之间交互的范围。只有在该失败可以复现，且其原因已充分隔离到足以指导回归测试和修复时，才算完成。