How do I ensure Python "zeros" memory when it is garbage collected?

I'm running into some trouble with memory management related to bytes in Python3.2. In some cases the ob_sval buffer seems to contain memory that I cannot account for.

For a particular secure application I need to be able to ensure that memory is "zeroed" and returned to the OS as soon as possible after it is no longer being used. Since re-compiling Python isn't really an option, I'm writing a module that can be used with LD_PRELOAD to:

Disable memory pooling by replacing PyObject_Malloc with PyMem_Malloc, PyObject_Realloc with PyMem_Realloc, and PyObject_Free with PyMem_Free (e.g.: what you would get if you compiled without WITH_PYMALLOC). I don't really care if the memory is pooled or not, but this seems to be the easiest approach.
Wraps malloc, realloc, and free so as to track how much memory is requested and to memset everything to 0 when it is released.

At a cursory glance, this approach seems to work great:

>>> from ctypes import string_at
>>> from sys import getsizeof
>>> from binascii import hexlify
>>> a = b"Hello, World!"; addr = id(a); size = getsizeof(a)
>>> print(string_at(addr, size))
b'\x01\x00\x00\x00\xd4j\xb2x\r\x00\x00\x00<J\xf6\x0eHello, World!\x00'
>>> del a
>>> print(string_at(addr, size))
b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x13\x00'

The errant \x13 at the end is odd but doesn't come from my original value so at first I assumed it was okay. I quickly found examples where things were not so good though:

>>> a = b'Superkaliphragilisticexpialidocious'; addr = id(a); size = getsizeof(a)
>>> print(string_at(addr, size))
b'\x01\x00\x00\x00\xd4j\xb2x#\x00\x00\x00\x9cb;\xc2Superkaliphragilisticexpialidocious\x00'
>>> del s
>>> print(string_at(addr, size))
b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00))\n\x00\x00ous\x00'

Here the last three bytes, ous, survived.

So, my question:

What's going on with the leftover bytes for bytes objects, and why don't they get deleted when del is called on them?

I'm guessing that my approach is missing something similar to a realloc, but I can't see what that would be in bytesobject.c.

I've attempted to quantify the number of 'leftover' bytes that remain after garbage collection and it appears to be predictable to some extent.

from collections import defaultdict
from ctypes import string_at
import gc
import os
from sys import getsizeof

def get_random_bytes(length=16):
    return os.urandom(length)

def test_different_bytes_lengths():
    rc = defaultdict(list)
    for ii in range(1, 101):
        while True:
            value = get_random_bytes(ii)
            if b'\x00' not in value:
                break
        check = [b for b in value]
        addr = id(value)
        size = getsizeof(value)
        del value
        gc.collect()
        garbage = string_at(addr, size)[16:-1]
        for jj in range(ii, 0, -1):
            if garbage.endswith(bytes(bytearray(check[-jj:]))):
                # for bytes of length ii, tail of length jj found
                rc[jj].append(ii)
                break
    return {k: len(v) for k, v in rc.items()}, dict(rc)

# The runs all look something like this (there is some variation):
# ({1: 2, 2: 2, 3: 81}, {1: [1, 13], 2: [2, 14], 3: [3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 83, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100]})
# That is:
#  - One byte left over twice (always when the original bytes object was of lengths 1 or 13, the first is likely because of the internal 'characters' list kept by Python)
#  - Two bytes left over twice (always when the original bytes object was of lengths 2 or 14)
#  - Three bytes left over in most other cases (the exact ones varies between runs but never has '12' in it)
# For added fun, if I replace the get_random_bytes call with one that returns an encoded string or random alphanumerics then results change slightly: lengths of 13 and 14 are now fully cleared too. My original test string was 13 bytes of encoded alphanumerics, of course!

Edit 1

I had originally expressed concern about the fact that if the bytes object is used in a function it doesn't get cleaned up at all:

>>> def hello_forever():
...     a = b"Hello, World!"; addr = id(a); size = getsizeof(a)
...     print(string_at(addr, size))
...     del a
...     print(string_at(addr, size))
...     gc.collect()
...     print(string_at(addr, size))
...     return addr, size
...
>>> addr, size = hello_forever()
b'\x02\x00\x00\x00\xd4J0x\r\x00\x00\x00<J\xf6\x0eHello, World!\x00'
b'\x01\x00\x00\x00\xd4J0x\r\x00\x00\x00<J\xf6\x0eHello, World!\x00'
b'\x01\x00\x00\x00\xd4J0x\r\x00\x00\x00<J\xf6\x0eHello, World!\x00'
>>> print(string_at(addr, size))
b'\x01\x00\x00\x00\xd4J0x\r\x00\x00\x00<J\xf6\x0eHello, World!\x00'

It turns out that this is an artificial concern that isn't covered by my requirements. You can see the comments to this question for details, but the problem comes from the way the hello_forever.__code__.co_consts tuple will contain a reference to Hello, World! even after a is deleted from the locals.

In the real code, the "secure" values would be coming from an external source and would never be hard-coded and later deleted like this.

Edit 2

I had also expressed confusion over the behaviour with strings. It has been pointed out that they likely also suffer the same problem as bytes with respect to hard-coding them in functions (e.g.: an artifact of my test code). There are two other risks with them that I have not been able to demonstrate as being a problem but will continue to investigate:

String interning is done by Python at various points to speed up access. This shouldn't be a problem since the interned strings are supposed to be removed when the last reference is lost. If it proves to be a concern it should be possible to replace PyUnicode_InternInPlace so that it doesn't do anything.
Strings and other 'primitive' object types in Python often keep a 'free list' to make it faster to get memory for new objects. If this proves to be a problem, the *_dealloc methods in the Objects/*.c can be replaced.

I had also believed that I was seeing a problem with class instances not getting zeroed correctly, but I now believe that was an error on my part.

Thanks

Much thanks to @Dunes and @Kevin for pointing out the issues that obfuscated my original question. Those issues have been left above in the "edit" sections above for reference.

Solution

It turns out that the problem was an absolutely stupid mistake in my own code that did the memset. I'm going to reach out to @Calyth, who generously added a bounty to this question, before 'accepting' this answer.

In short and simplified, the malloc/free wrapper functions work like this:

Code calls malloc asking for N bytes of memory.
- The wrapper calls the real function but asks for N+sizeof(size_t) bytes.
- It writes N to the beginning of the range and returns an offset pointer.
Code uses the offset pointer, oblivious to the fact that it is attached to a slightly larger chunk of memory than was requested.
Code calls free asking to return the memory and passing in that offset pointer.
- The wrapper looks before the offset pointer to get the originally requested size of memory.
- It calls memset to ensure everything is set to zero (the library is compiled without optimization to prevent the compiler from ignoring the memset).
- Only then does it call the real function.

My mistake was calling the equivalent of memset(actual_pointer, 0, requested_size) instead of memset(actual_pointer, 0, actual_size).

I'm now facing the mind-boggling question of why there weren't always '3' leftover bytes (my unit tests verify that none of my randomly generated bytes objects contain any nulls) and why strings would not also have this problem (does Python over-allocate the size of the string buffer, perhaps). Those, however, are problems for another day.

The upshot of all of this, is that it turns out to be relatively easy to ensure that bytes and strings are set to zero once they are garbage collected! (There are a bunch of caveats about hard-coded strings, free lists, and so forth so anyone else who is trying to do this should read the original question, the comments on the question, and this 'answer' carefully.)