New changeset 53e4c91725083975598350877e2ed8e2d0194114 by Dong-hee Na in branch 'master':
bpo-40077: Convert _abc module to use PyType_FromSpec() (GH-19202)
https://github.com/python/cpython/commit/53e4c91725083975598350877e2ed8e2d0194114

This change introduced a reference leak:

$ ./python -m test -R 3:3 test_threading -m test.test_threading.SubinterpThreadingTests.test_threads_join_2
0:00:00 load avg: 1.52 Run tests sequentially
0:00:00 load avg: 1.52 [1/1] test_threading
beginning 6 repetitions
123456
......
test_threading leaked [19, 19, 19] references, sum=57
test_threading leaked [12, 12, 12] memory blocks, sum=36
test_threading failed

== Tests result: FAILURE ==

1 test failed:
    test_threading

Total duration: 768 ms
Tests result: FAILURE

Attached test_leak.py is enough to reproduce the leak. It's related to subinterpreters and the _abc module.

I'm not sure why, but trigger explicitly a second GC collection fix the issue.

diff --git a/Python/pylifecycle.c b/Python/pylifecycle.c
index 2d5cb0ff78..d20ae01238 100644
--- a/Python/pylifecycle.c
+++ b/Python/pylifecycle.c
@@ -1295,6 +1295,7 @@ finalize_interp_clear(PyThreadState *tstate)
     /* Trigger a GC collection on subinterpreters*/
     if (!is_main_interp) {
         _PyGC_CollectNoFail();
+        _PyGC_CollectNoFail();
     }
 
     finalize_interp_types(tstate, is_main_interp);

FYI,
first gc collect 772
secondary gc collect 4

gc: collectable <type 0x7fc033c3cbd0>
gc: collectable <dict 0x104d79830>
gc: collectable <tuple 0x104d725a0>
gc: collectable <builtin_function_or_method 0x104d79890>

is not collected for the first time.

Running 
from abc import ABCMeta
on the subinterpreter makes same size of leak.

New changeset 9cc3ebd7e04cb645ac7b2f372eaafa7464e16b9c by Victor Stinner in branch 'master':
bpo-40149: Implement traverse in _abc._abc_data (GH-19412)
https://github.com/python/cpython/commit/9cc3ebd7e04cb645ac7b2f372eaafa7464e16b9c

In _abcmodule_exec(), when _abc_data type is created, it's created with refcnt=3:
* 1 strong reference (normal)
* +1 ref from tp_dict['__new__'] slot
* +1 ref from tp_mro

type_traverse() visits tp_dict and tp_mro, so it's fine.

In Py_EndInterpreter(), PyInterpreterState_Clear() clears os.register_atfork() callbacks which were one of the last references to _abc_data type. The first call to _PyGC_CollectNoFail() destroys _abc_data *instances* but not the _abc_data type.

The following patch works around the issue:

diff --git a/Modules/_abc.c b/Modules/_abc.c
index 1efc98bf72..410dbcf96a 100644
--- a/Modules/_abc.c
+++ b/Modules/_abc.c
@@ -54,6 +54,7 @@ typedef struct {
 static int
 abc_data_traverse(_abc_data *self, visitproc visit, void *arg)
 {
+    Py_VISIT(Py_TYPE(self));
     Py_VISIT(self->_abc_registry);
     Py_VISIT(self->_abc_cache);
     Py_VISIT(self->_abc_negative_cache);


$ ./python -m test -R 3:3 test_threading -m test.test_threading.SubinterpThreadingTests.test_threads_join_2
(...)
Tests result: SUCCESS


I'm not sure why Py_VISIT(Py_TYPE(self)) is needed. Maybe it's a regression caused by commit 364f0b0f19cc3f0d5e63f571ec9163cf41c62958 of bpo-35810.

It sems like the GC doesn't take in account that instances of types allocated on the heap (if type->tp_flags has the Py_TPFLAGS_HEAPTYPE flag) hold a strong refeference to the type (PyObject.ob_type).

I created bpo-40217: "The garbage collector doesn't take in account that objects of heap allocated types hold a strong reference to their type".

Wow Thank you for the summary :)

> bpo-40149: Implement traverse in _abc._abc_data (GH-19412)

Pablo told me that this change is not correct: the overriden traverse function must call PyType_Type.tp_traverse (parent method).

> I created bpo-40217: "The garbage collector doesn't take in account that objects of heap allocated types hold a strong reference to their type".

This issue is now fixed. I tested manually: I confirm that it does fix the test_threading leak, so I close the issue.

$ ./python -m test -R 3:3 test_threading
(...)
== Tests result: SUCCESS ==

1 test OK.

Total duration: 1 min 14 sec
Tests result: SUCCESS