ANTsX
potential bug: reference leak when torch is loaded and a function errors
When torch is loaded and a function errors, there is a reference leak reported when the ipython console is exited. This does not seem to happen in a normal python console and only when torch is loaded. Very weird.. I've seen this a few other times but never reproducible so unsure if it's the same issue or if there's a general reference leak.
import ants
import torch
img = ants.image_read(ants.get_data('r16'))
img.crop_indices([0,0],[10,1000])
Then exit() and you get this:
nanobind: leaked 1 instances!
- leaked instance 0x13362a208 of type "AntsImageF2"
nanobind: leaked 1 types!
- leaked type "ants.lib.AntsImageF2"
nanobind: leaked 1 functions!
- leaked function "cropImage"
nanobind: this is likely caused by a reference counting issue in the binding code.
Seems to be something with pytorch and third-party modules generally - e.g. https://github.com/python/cpython/issues/98253. Probably not a big issue but still worrying.
See also nanobind FAQ on the issue https://nanobind.readthedocs.io/en/latest/faq.html#why-am-i-getting-errors-about-leaked-functions-and-types
Got the same issue and memory keeps building up until shutting down the program. Found a previous issue https://github.com/ANTsX/ANTsPy/issues/117, and it seems that their example code also has memory leaks in 0.5.4.
antsRegistration -d 2 -r [0x13fc74ce8,0x13fc74d08,1] -m mattes[0x13fc74ce8,0x13fc74d08,1,32,regular,0.2] -t Affine[0.25] -c 2100x1200x1200x0 -s 3x2x1x0 -f 4x2x2x1 -x [NA,NA] -m mattes[0x13fc74ce8,0x13fc74d08,1,32] -t SyN[0.200000,3.000000,0.000000] -c [40x20x0,1e-7,8] -s 2x1x0 -f 4x2x1 -u 1 -z 1 -o [/var/folders/bs/n0q8wqv931g89ppshhgp2m2m0000gn/T//RtmpbpYhz2/filea3bb284caaea,0x13fc74ca8,0x13fc74cc8] -x [NA,NA] --float 1 --write-composite-transform 0 -v 1
nanobind: leaked 9 instances!
- leaked instance 0x13fc74a08 of type "ants.lib.AntsImageF2"
- leaked instance 0x13fc749c8 of type "ants.lib.AntsTransformF22"
- leaked instance 0x13fc74be8 of type "ants.lib.AntsImageF2"
- leaked instance 0x13fc747a8 of type "ants.lib.AntsImageF2"
- leaked instance 0x13fc74828 of type "ants.lib.AntsImageF2"
- leaked instance 0x13fc74ae8 of type "ants.lib.AntsImageF2"
- leaked instance 0x13fc74a68 of type "ants.lib.AntsTransformF22"
- leaked instance 0x13fc747c8 of type "ants.lib.AntsImageF2"
- leaked instance 0x13dd27828 of type "ants.lib.AntsTransformF33"
nanobind: leaked 3 types!
- leaked type "ants.lib.AntsImageF2"
- leaked type "ants.lib.AntsTransformF33"
- leaked type "ants.lib.AntsTransformF22"
nanobind: this is likely caused by a reference counting issue in the binding code.
>>> ants.__version__
'0.5.4'
Got the same issue and memory keeps building up until shutting down the program. Found a previous issue https://github.com/ANTsX/ANTsPy/issues/117, and it seems that their example code also has memory leaks in 0.5.4.
Can you please post a reproducible example?
There was also a report of something similar in #678 - the user appears to have deleted their comments but it was something about running registrations in a loop. I tried reporting memory usage in a loop but it appeared to increase a lot then only very slightly after the first iteration. Hard to tell if it was a small leak or just background optimization processes. Or maybe Python was not reporting memory correctly.
Will definitely investigate further if there's an example, ideally using built-in antspy data or failing that some other public data
I can't get the torch warnings on my Intel Mac
Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 15:55:29) [Clang 17.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import ants
>>> import torch
>>> img = ants.image_read(ants.get_data('r16'))
>>> img.crop_indices([0,0],[10,1000])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/Caskroom/miniforge/base/envs/antspy_torch/lib/python3.12/site-packages/ants/decorators.py", line 7, in wrapper
return func(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/Caskroom/miniforge/base/envs/antspy_torch/lib/python3.12/site-packages/ants/ops/crop_image.py", line 110, in crop_indices
itkimage = libfn(image.pointer, image.pointer, 1, 2, lowerind, upperind)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: /Users/runner/work/ANTsPy/ANTsPy/itksource/Modules/Core/Common/src/itkDataObject.cxx:367:
Requested region is (at least partially) outside the largest possible region.
>>> exit()
torch == 2.2.2 antspyx == 0.5.4
Leaving this thread for the torch issue. For general memory leak problems, please see #733.
For some reasons when I run in bare python in terminal, it doesn't complain about the memory leaks. However, the memory leak still persists. For example, the following example keeps occupying more memories (activity monitor shows 7GB RAM usage after a few hundred iters. However, the diff of memory table shows nothing (signs of mem leak).
My suspect of nanobind warning is that because we use python IDE, and IDE keeps a weak ref to the python objects. If the object is not cleared on exit, then nanobind will raise the warning. I'll try to capture a reproducible example when I get back.
import ants
import numpy as np
img = np.random.random((400, 400))
img_ants = ants.image_clone(ants.from_numpy(img), pixeltype='float')
from pympler.tracker import SummaryTracker
tracker = SummaryTracker()
for i in range(5000):
ants.image_similarity(img_ants, img_ants, metric_type='Correlation')
if i % 100 == 0:
# expect no change in memory table, but increased memory usage
print(tracker.print_diff())
Leaving this thread for the torch issue. For general memory leak problems, please see #733.
Oh just saw your message. Thanks for reference. I'll dig more into this (indeed we need reproducible example but this is tricky)
Thanks @dipterix , this tracks with what I found previously - Python doesn't think it's using the memory, I think there's leftover C++ objects.