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Posted to github@arrow.apache.org by "chunyang (via GitHub)" <gi...@apache.org> on 2024/03/07 23:22:15 UTC
[PR] GH-37989: [C++] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
chunyang opened a new pull request, #40412:
URL: https://github.com/apache/arrow/pull/40412
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### Rationale for this change
When creating Arrow arrays using `pa.array` from lists of dicts, memory usage is observed to increase over time even despite the created arrays going out of scope. The issue appears to only happen for lists of dicts, as opposed to lists of numpy arrays or other types.
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### What changes are included in this PR?
This PR makes two changes to _python_to_arrow.cc_, to ensure that new references created by [`PyDict_Items`](https://docs.python.org/3/c-api/dict.html#c.PyDict_Items) and [`PySequence_GetItem`](https://docs.python.org/3/c-api/sequence.html#c.PySequence_GetItem) are properly reference counted via `OwnedRef`.
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### Are these changes tested?
The change was tested against the following reproduction script:
```python
"""Repro memory increase observed when creating pyarrow arrays."""
# System imports
import logging
# Third-party imports
import numpy as np
import psutil
import pyarrow as pa
LIST_LENGTH = 5 * (2**20)
LOGGER = logging.getLogger(__name__)
def initialize_logging() -> None:
logging.basicConfig(
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
level=logging.INFO,
)
def get_rss_in_mib() -> float:
"""Return the Resident Set Size of the current process in MiB."""
return psutil.Process().memory_info().rss / 1024 / 1024
def main() -> None:
initialize_logging()
for idx in range(100):
data = np.random.randint(256, size=(LIST_LENGTH,), dtype=np.uint8)
# data = "a" * LIST_LENGTH
pa.array([{"data": data}])
if (idx + 1) % 10 == 0:
LOGGER.info(
"%d dict arrays created, RSS: %.2f MiB", idx + 1, get_rss_in_mib()
)
LOGGER.info("---------")
for idx in range(100):
pa.array(
[
np.random.randint(256, size=(LIST_LENGTH,), dtype=np.uint8).tobytes(),
]
)
if (idx + 1) % 10 == 0:
LOGGER.info(
"%d non-dict arrays created, RSS: %.2f MiB", idx + 1, get_rss_in_mib()
)
if __name__ == "__main__":
main()
```
Prior to this change, the reproduction script produces the following output:
```
2024-03-07 23:14:17,560 - __main__ - INFO - 10 dict arrays created, RSS: 121.05 MiB
2024-03-07 23:14:17,698 - __main__ - INFO - 20 dict arrays created, RSS: 171.07 MiB
2024-03-07 23:14:17,835 - __main__ - INFO - 30 dict arrays created, RSS: 221.09 MiB
2024-03-07 23:14:17,971 - __main__ - INFO - 40 dict arrays created, RSS: 271.11 MiB
2024-03-07 23:14:18,109 - __main__ - INFO - 50 dict arrays created, RSS: 320.86 MiB
2024-03-07 23:14:18,245 - __main__ - INFO - 60 dict arrays created, RSS: 371.65 MiB
2024-03-07 23:14:18,380 - __main__ - INFO - 70 dict arrays created, RSS: 422.18 MiB
2024-03-07 23:14:18,516 - __main__ - INFO - 80 dict arrays created, RSS: 472.20 MiB
2024-03-07 23:14:18,650 - __main__ - INFO - 90 dict arrays created, RSS: 522.21 MiB
2024-03-07 23:14:18,788 - __main__ - INFO - 100 dict arrays created, RSS: 572.23 MiB
2024-03-07 23:14:18,789 - __main__ - INFO - ---------
2024-03-07 23:14:19,001 - __main__ - INFO - 10 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:19,211 - __main__ - INFO - 20 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:19,417 - __main__ - INFO - 30 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:19,623 - __main__ - INFO - 40 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:19,832 - __main__ - INFO - 50 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:20,047 - __main__ - INFO - 60 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:20,253 - __main__ - INFO - 70 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:20,499 - __main__ - INFO - 80 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:20,725 - __main__ - INFO - 90 non-dict arrays created, RSS: 567.61 MiB
2024-03-07 23:14:20,950 - __main__ - INFO - 100 non-dict arrays created, RSS: 567.61 MiB
```
After this change, the output changes to the following. Notice that the Resident Set Size (RSS) no longer increases as more Arrow arrays are created from list of dict.
```
2024-03-07 23:14:47,246 - __main__ - INFO - 10 dict arrays created, RSS: 81.73 MiB
2024-03-07 23:14:47,353 - __main__ - INFO - 20 dict arrays created, RSS: 76.53 MiB
2024-03-07 23:14:47,445 - __main__ - INFO - 30 dict arrays created, RSS: 82.20 MiB
2024-03-07 23:14:47,537 - __main__ - INFO - 40 dict arrays created, RSS: 86.59 MiB
2024-03-07 23:14:47,634 - __main__ - INFO - 50 dict arrays created, RSS: 80.28 MiB
2024-03-07 23:14:47,734 - __main__ - INFO - 60 dict arrays created, RSS: 85.44 MiB
2024-03-07 23:14:47,827 - __main__ - INFO - 70 dict arrays created, RSS: 85.44 MiB
2024-03-07 23:14:47,921 - __main__ - INFO - 80 dict arrays created, RSS: 85.44 MiB
2024-03-07 23:14:48,024 - __main__ - INFO - 90 dict arrays created, RSS: 82.94 MiB
2024-03-07 23:14:48,132 - __main__ - INFO - 100 dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,132 - __main__ - INFO - ---------
2024-03-07 23:14:48,229 - __main__ - INFO - 10 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,324 - __main__ - INFO - 20 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,420 - __main__ - INFO - 30 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,516 - __main__ - INFO - 40 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,613 - __main__ - INFO - 50 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,710 - __main__ - INFO - 60 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,806 - __main__ - INFO - 70 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:48,905 - __main__ - INFO - 80 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:49,009 - __main__ - INFO - 90 non-dict arrays created, RSS: 87.84 MiB
2024-03-07 23:14:49,108 - __main__ - INFO - 100 non-dict arrays created, RSS: 87.84 MiB
```
When this change is tested against the reproduction script provided in https://github.com/apache/arrow/issues/37989#issue-1924129600, the reported memory increase is no longer observed.
I have not added a unit test, but it may be possible to add one similar to the reproduction scripts used above, provided there's an accurate way to capture process memory usage on all the platforms that Arrow supports, and provided memory usage is not affected by concurrently running tests. If this code could be tested under valgrind, that may be an even better way to go.
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### Are there any user-facing changes?
None
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "jakirkham (via GitHub)" <gi...@apache.org>.
jakirkham commented on PR #40412:
URL: https://github.com/apache/arrow/pull/40412#issuecomment-2058537295
In that case, maybe we can just patch the conda-forge packages
Thought this might help more users with this issue (like wheel consumers), but understand if that is not feasible
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "pitrou (via GitHub)" <gi...@apache.org>.
pitrou commented on code in PR #40412:
URL: https://github.com/apache/arrow/pull/40412#discussion_r1517490377
##########
python/pyarrow/src/arrow/python/python_to_arrow.cc:
##########
@@ -1114,6 +1115,7 @@ class PyStructConverter : public StructConverter<PyConverter, PyConverterTrait>
Result<std::pair<PyObject*, PyObject*>> GetKeyValuePair(PyObject* seq, int index) {
PyObject* pair = PySequence_GetItem(seq, index);
+ OwnedRef pair_ref(pair);
Review Comment:
Should be moved just below `RETURN_IF_PYERROR`.
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "galipremsagar (via GitHub)" <gi...@apache.org>.
galipremsagar commented on PR #40412:
URL: https://github.com/apache/arrow/pull/40412#issuecomment-2057497401
@pitrou | @jorisvandenbossche Is it possible to back-port this fix for `14.x` and `15.x` versions of pyarrow?
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "jorisvandenbossche (via GitHub)" <gi...@apache.org>.
jorisvandenbossche commented on PR #40412:
URL: https://github.com/apache/arrow/pull/40412#issuecomment-2058422698
@galipremsagar we are currently in the process of releasing pyarrow 16.0, and I think it is quite unlikely that we will still do a patch release for 14.0 and 15.0 (given the work involved to do a release at the moment)
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "chunyang (via GitHub)" <gi...@apache.org>.
chunyang commented on code in PR #40412:
URL: https://github.com/apache/arrow/pull/40412#discussion_r1518093338
##########
python/pyarrow/src/arrow/python/python_to_arrow.cc:
##########
@@ -1114,6 +1115,7 @@ class PyStructConverter : public StructConverter<PyConverter, PyConverterTrait>
Result<std::pair<PyObject*, PyObject*>> GetKeyValuePair(PyObject* seq, int index) {
PyObject* pair = PySequence_GetItem(seq, index);
+ OwnedRef pair_ref(pair);
Review Comment:
Thanks for the review! I made the suggested move.
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #40412:
URL: https://github.com/apache/arrow/pull/40412#issuecomment-1984771654
:warning: GitHub issue #37989 **has been automatically assigned in GitHub** to PR creator.
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Re: [PR] GH-37989: [C++] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "github-actions[bot] (via GitHub)" <gi...@apache.org>.
github-actions[bot] commented on PR #40412:
URL: https://github.com/apache/arrow/pull/40412#issuecomment-1984770111
:warning: GitHub issue #37989 **has been automatically assigned in GitHub** to PR creator.
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "jorisvandenbossche (via GitHub)" <gi...@apache.org>.
jorisvandenbossche merged PR #40412:
URL: https://github.com/apache/arrow/pull/40412
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Re: [PR] GH-37989: [Python] Plug reference leaks when creating Arrow array from Python list of dicts [arrow]
Posted by "conbench-apache-arrow[bot] (via GitHub)" <gi...@apache.org>.
conbench-apache-arrow[bot] commented on PR #40412:
URL: https://github.com/apache/arrow/pull/40412#issuecomment-2002279856
After merging your PR, Conbench analyzed the 7 benchmarking runs that have been run so far on merge-commit 03c771a6269663eca376ca4e95f86aaaebc9f10b.
There were no benchmark performance regressions. 🎉
The [full Conbench report](https://github.com/apache/arrow/runs/22746864594) has more details. It also includes information about 3 possible false positives for unstable benchmarks that are known to sometimes produce them.
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