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This bug is similar to the importlock deadlock, and it's really part of
a larger problem that you should release all locks before you fork. 
However, we can fix this in the threading module directly by freeing and
resetting the locks on the main thread after a fork.
I've attached a test case that inserts calls to sleep at the right
places to make the following occur:
- Main thread spawns a worker thread.
- Main thread joins worker thread.
- To join, the main thread acquires the lock on the condition variable
(worker.__block.acquire()).
== switch to worker ==
- Worker thread forks.
== switch to child process ==
- Worker thread, which is now the only thread in the process, returns.
- __bootstrap_inner calls self.__stop() to notify any other threads
waiting for it that it returned.
- __stop() tries to acquire self.__block, which has been left in an
acquired state, so the child process hangs here.
== switch to worker in parent process ==
- Worker thread calls os.waitpid(), which hangs, since the child never
returns.
So there's the deadlock.
I think I should be able to fix it just by resetting the condition
variable lock and any other locks hanging off the only thread left
standing after the fork.

Here's a patch for 3.2 which adds the fix and a test case. I also
verified that the problem exists in 3.1, 2.7, and 2.6 and backported the
patch to those versions, but someone should review this one before I
upload those.

Here's an updated patch for py3k (3.2). The test still fails without the fix, and passes with the fix.
Thinking more about this, I'll try summarizing the bug more coherently:
When the main thread joins the child threads, it acquires some locks. If a fork in a child thread occurs while those locks are held, they remain locked in the child process. My solution is to do here what we do elsewhere in CPython: abandon radioactive locks and allocate fresh ones.

I realized that in a later fix for unladen-swallow, we also cleared the condition variable waiters list, since it has radioactive synchronization primitives in it as well.
Here's an updated patch that simplifies the fix by just using __init__() to completely reinitialize the condition variables and adds a test.
This corresponds to unladen-swallow revisions r799 and r834.

I don't have any direct opinions on this, as it is just a bandaid. fork, as defined by POSIX, doesn't allow what we do with it, so we're reliant on great deal of OS and library implementation details. The only portable and robust solution would be to replace it with a unified fork-and-exec API that's implemented directly in C.

I completely agree, but the cat is out of the bag on this one. I don't see how we could get rid of fork until Py4K, and even then I'm sure there will be people who don't want to see it go, and I'd rather not spend my time arguing this point.
The only application of fork that doesn't use exec that I've heard of is pre-forked Python servers. But those don't seem like they would be very useful, since with refcounting the copy-on-write behavior doesn't get you very many wins.
The problem that this bandaid solves for me is that test_threading.py already tests thread+fork behaviors, and can fail non-deterministically.
This problem was exacerbated while I was working on making the compilation thread.
I don't think we can un-support fork and threads in the near future either, because subprocess.py uses fork, and libraries can use fork behind the user's back.

fwiw a unified fork-and-exec API implemented in C is what I added in Modules/_posixsubprocess.c to at least avoid this issue as much as possible when using subprocess.

patch looks good. committed in r87710 for 3.2. needs back porting to 3.1 and 2.7 and optionally 2.6.

r87726 for release31-maint
r87727 for release27-maint - this required a bit more fiddling as _block and _started and _cond were __ private.

Attached is a patch for Python 2.6 release26_maint for reference incase someone wants it. That branch is closed - security fixes only.

r87710 introduces an AttributeError in test_thread's TestForkInThread test case. If os.fork() is called from a thread created by the _thread module, threading._after_fork() will get a _DummyThread (with no _block attribute) as the current thread.
I've attached a patch that checks whether the thread has a _block attribute before trying to reinitialize it.

eek, thanks for noticing that!
r87740 fixes this in py3k. backporting to 3.1 and 2.7 now.

r87741 3.1
r87742 2.7

Python version: 2.7.5
OS: Solaris 9
I'm still observing this issue (or Issue5114) on Solaris 9. The symptom is that test_threading hangs indefinitely (tested: overnight) and running pstack on the process, I'm seeing:
----------------- lwp# 1 / thread# 1 --------------------
 ff3dc734 lwp_park (0, 0, 0)
 ff3d3c74 s9_lwp_park (0, 0, 0, 1, feed4f48, 18f5a4) + 28
 ff3dc698 s9_handler (0, 0, 0, 1, feed4f48, 18f5a4) + 90
 ff1dea70 _sema_wait (0, feee66a0, fed6b054, feee6000, 2a298478, d1f20) + 1d4
 ff1dec30 sema_wait (81aa8, ff1dec24, 722a5b4b, 1101c, feed4f48, 134d60) + c
 feed4f48 sem_wait (81aa8, 0, fed6b1ac, 0, 0, 1) + 20
 ff050890 PyThread_acquire_lock (81aa8, 1, fed6b214, 2, 0, 1ae778) + 5c
 ff05524c lock_PyThread_acquire_lock (0, 22030, 0, 13ee40, 16a298, 55150) + 50
 fefa779c PyCFunction_Call (1ae788, 22030, 0, ff0d8eb8, 55150, ff0551fc) + e4
 ff016b14 PyEval_EvalFrameEx (18f5a0, 0, 0, d4f66, 16a298, 22030) + 5ee8
 ff0185d0 PyEval_EvalCodeEx (12c968, 0, 18f5a0, 4, 1, 18f5a4) + 924
 ff0168f8 PyEval_EvalFrameEx (1902b8, 0, 1, 1765c0, 16a298, 1b12d0) + 5ccc
 ff0185d0 PyEval_EvalCodeEx (13f608, 0, 1902b8, 4, 1, 1902bc) + 924
 ff0168f8 PyEval_EvalFrameEx (154748, 0, 1, 31f7f, 16a298, 1b1250) + 5ccc
 ff0185d0 PyEval_EvalCodeEx (10d650, 54a50, 154748, 2203c, 0, 2203c) + 924
 fef8e11c function_call (22038, 22030, 1386f0, 2203c, 130730, 22030) + 168
 fef604e8 PyObject_Call (130730, 22030, 1386f0, ff0e0340, fef8dfb4, 0) + 60
 ff0137dc PyEval_EvalFrameEx (169110, 0, 22030, 10e62d, 16a298, 22030) + 2bb0
 ff017478 PyEval_EvalFrameEx (168f80, 0, 169114, 1769fa, 16a298, 16a298) + 684c
 ff017478 PyEval_EvalFrameEx (176cb0, 0, 168f84, 12a2c0, 16a298, 16a298) + 684c
 ff0185d0 PyEval_EvalCodeEx (13f410, 176cb4, 176cb0, 13433c, 1, 0) + 924
 fef8e040 function_call (1b26f0, 134330, 0, ff1bc000, 1b26f0, 0) + 8c
 fef604e8 PyObject_Call (1b26f0, 134330, 0, ff0e0340, fef8dfb4, 134320) + 60
 fef6e530 instancemethod_call (0, 134330, 0, 0, 1b26f0, 134bd0) + a4
 fef604e8 PyObject_Call (c3b48, 22030, 0, ff0e0340, fef6e48c, 0) + 60
 ff01051c PyEval_CallObjectWithKeywords (c3b48, 22030, 0, 0, 0, 0) + 68
 ff05568c t_bootstrap (63bd0, 0, 0, 0, 16a298, ff0e2804) + 4c
 ff1e53a4 _lwp_start (0, 0, 0, 0, 0, 0)
----------------- lwp# 2 / thread# 2 --------------------
 ff3dc734 lwp_park (0, 0, 0)
 ff3d3c74 s9_lwp_park (0, 0, 0, 1, b64a0d58, 136818) + 28
 ff3dc698 s9_handler (0, 0, 0, 1, b64a0d58, 136818) + 90
 ff1dea70 _sema_wait (0, feee66a0, fec6b054, feee6000, 2a298478, d1f20) + 1d4
 ff1dec30 sema_wait (8ab00, ff1dec24, 722a5b4b, 1101c, feed4f48, 134d60) + c
 feed4f48 sem_wait (8ab00, 0, fec6b1ac, 0, 0, 1) + 20
 ff050890 PyThread_acquire_lock (8ab00, 1, fec6b214, 2, 0, 1ae610) + 5c
 ff05524c lock_PyThread_acquire_lock (0, 22030, 0, 13ee40, 156168, 55160) + 50
 fefa779c PyCFunction_Call (1ae620, 22030, 0, ff0d8eb8, 55160, ff0551fc) + e4
 ff016b14 PyEval_EvalFrameEx (18fe60, 0, 0, d4f66, 156168, 22030) + 5ee8
 ff0185d0 PyEval_EvalCodeEx (12c968, 0, 18fe60, 4, 1, 18fe64) + 924
 ff0168f8 PyEval_EvalFrameEx (18fce8, 0, 1, 1765c0, 156168, 1b11b0) + 5ccc
 ff0185d0 PyEval_EvalCodeEx (13f608, 0, 18fce8, 4, 1, 18fcec) + 924
 ff0168f8 PyEval_EvalFrameEx (18fb88, 0, 1, 136155, 156168, 1a2930) + 5ccc
 ff0185d0 PyEval_EvalCodeEx (48b60, 18fb8c, 18fb88, 19d41c, 1, 2203c) + 924
 fef8e11c function_call (22038, 19d410, 1b3c00, 2203c, 130370, 22030) + 168
 fef604e8 PyObject_Call (130370, 19d410, 1b3c00, ff0e0340, fef8dfb4, 19d400) + 60
 ff0137dc PyEval_EvalFrameEx (18fa20, 0, 19d410, 10e62d, 156168, 134950) + 2bb0
 ff017478 PyEval_EvalFrameEx (18f890, 0, 18fa24, 1769fa, 156168, 156168) + 684c
 ff017478 PyEval_EvalFrameEx (18f728, 0, 18f894, 12a2c0, 156168, 156168) + 684c
 ff0185d0 PyEval_EvalCodeEx (13f410, 18f72c, 18f728, 19d3fc, 1, 0) + 924
 fef8e040 function_call (1b26f0, 19d3f0, 0, ff1bc000, 1b26f0, 0) + 8c
 fef604e8 PyObject_Call (1b26f0, 19d3f0, 0, ff0e0340, fef8dfb4, 19d3e0) + 60
 fef6e530 instancemethod_call (0, 19d3f0, 0, 0, 1b26f0, 1b1250) + a4
 fef604e8 PyObject_Call (1aeaf8, 22030, 0, ff0e0340, fef6e48c, 0) + 60
 ff01051c PyEval_CallObjectWithKeywords (1aeaf8, 22030, 0, 0, 0, 0) + 68
 ff05568c t_bootstrap (63c30, 0, 0, 0, 156168, ff0e2804) + 4c
 ff1e53a4 _lwp_start (0, 0, 0, 0, 0, 0)
The problem does not occur on Solaris 10.