CoW: Use weakref callbacks to track dead references

[wangwillian0]

• closes PERF: hash_pandas_object performance regression between 2.1.0 and 2.1.1 #55245
• Tests added and passed if fixing a bug or adding a new feature
• All code checks passed.
• Added type annotations to new arguments/methods/functions.
• Added an entry in the latest doc/source/whatsnew/vX.X.X.rst file if fixing a bug or adding a new feature.

This is an alternative solution to #55518. What it happening here:

• Uses the weakref.ref callback to count the number of dead references present at the referenced_blocks list.
• Takes 20% more time at the constructor because of the function declaration!
  • The function declaration can be moved to the add_reference and add_index_reference, but this is just moving the performance hit to these methods.
• Everything is O(1) now, including has_reference. (_clear_dead_references is amortized to O(1))
• If the number of dead references is more than 256 and +50% of the array, it will prune these references
  • The implication is that the linear slow dead reference cleaning happens next to the GC calls, which I think this is a more intuitive behavior.

(also check another possibilities at #55008)

Let me know if I should continue working on this solution.

[WillAyd]

Is this ever reachable without the GIL? This doesn't appear thread safe so thinking through what impacts that might have

[wangwillian0]

Sorry, can you explain a bit more? Is pandas preparing to be thread-safe and use the no-GIL feature of the coming python version?

[WillAyd]

We release the GIL in quite a few places in the Cython code today, mostly for downstream libraries like Dask to take advantage of. Though I guess this in its current state wouldn't work without the GIL since it is already using weakref on main

[WillAyd]

Assuming this is an alternate solution to @phofl PR in #55518

[phofl]

#55518 needs to be back ported. This is something that we can consider for main and 2.2, but I want to test this more before we rely on it.

[wangwillian0]

I just fixed the tests. Any thoughts about it @phofl @WillAyd?

[WillAyd]

Generally looks good though will defer to @phofl who is more familiar with this. I think he is traveling this week so thanks for your patience in advance

[WillAyd]

Not sure of all of the impacts but I think cinit is mostly used for C-level structures. I think setting this callback should instead be done in init

[wangwillian0]

I just updated it

[wangwillian0]

Actually, it's doesn't work because cinit is called before init, so we need the callback ready there, unless we move everything to init. I changed it back 😅

[WillAyd]

Hmm OK. And this definitely doesn't cause any memory leaks or issues with reference counting then right?

[wangwillian0]

It should be correct as long as the reference list is not modified manually without the classes methods or run under concurrency.

Another thing is that taking the length of the list of refs directly won't give the correct length too (the actual value is len(referenced_blocks) - dead_counter). From what I looked, the exact length was never used anywhere else in the code right now, but I can implement the len method if needed.

If someone modified the list manually without the classes methods, the counter would be wrong and the memory consumption could grow a lot (just like the current solution at main) and the has_reference() will be plain wrong.

[wangwillian0]

Sorry, I meant multi threading

[phofl]

Yes I understood this, but again, this is a realistic scenario

[wangwillian0]

The problem would be that self.dead_counter += 1 isn't atomic. I can add a lock to it but, correct if I'm wrong, the rest of the code isn't thread-safe too. e.g. list comprehension from _clear_dead_references doesn't seem to be thread-safe

[wangwillian0]

Here is a sample of how _clear_dead_references is not really thread safe:

import threading
class Test:
    def __init__(self):
        self.v = list(range(1000))

    def add(self, x):
        self.v.append(x)

    def rebuild(self):
        self.v = [x for x in self.v]
    
    def simulate(self):
        for _ in range(1000):
            self.add(1)
            self.rebuild()
    
    def race(self):
        threads = [threading.Thread(target=self.simulate) for _ in range(10)]
        for t in threads:
            t.start()
        for t in threads:
            t.join()
        print(len(self.v))

test1 = Test()
test2 = Test()
test1.race()
test2.race()

I couldn't reproduce the same with pandas code, but I think it's more about timing than something else. The point is, is this class supposed to be thread-safe?

[phofl]

Nope that works, was just not sure if I was missing something obvious

[wangwillian0]

Any news?

[mroeschke]

Personally I would be more partial to exploring #55631 (IMO I think the mental model of using a set would be simpler)

[phofl]

Can you run the ctors.py benchmarks?

[wangwillian0]

Sorry for the delay. Here are the benchmarks:

Change	Before [593fa85]	After [98addad]	Ratio	Benchmark (Parameter)
+	5.74±0.2ms	7.37±0.2ms	1.29	frame_ctor.FromArrays.time_frame_from_arrays_int
+	7.65±0.08ms	8.63±0.2ms	1.13	frame_ctor.FromArrays.time_frame_from_arrays_sparse
+	1.43±0.07ms	1.47±0.06ms	1.03	frame_ctor.FromRecords.time_frame_from_records_generator(1000)

[phofl]

How does this correspond to the other timings in the issue?

[wangwillian0]

How does this correspond to the other timings in the issue?

Not sure if I fully understand what is being asked, but this ~20% increase is from the overhead in the constructor. What this PR will be better is mainly at has_reference, which will be O(1) independently of the number of references. Insertions also should be a little faster because there is no periodic calls to the cleanings method, but this is probably not meaningful in any way,

[wangwillian0]

Updates?

[github-actions]

This pull request is stale because it has been open for thirty days with no activity. Please update and respond to this comment if you're still interested in working on this.

[wangwillian0]

Hey @phofl, what is the current status of this PR?

[wangwillian0]

@phofl?

[wangwillian0]

Hi, @phofl, can you give an update?