"import numpy" leaks - reported by valgrind

Reproducing code example:

PYTHONMALLOC=malloc valgrind --leak-check=full --show-leak-kinds=definite --suppressions=pybind11/tests/valgrind-python.supp --gen-suppressions=all python3.9-dbg -c "import numpy; print(numpy.__version__)"

Error message:

The output is fairly long, so I made a gist: https://gist.github.com/bstaletic/061ea8912ed5bc4e238363a120f70a1c The suppression file is in the gist as well.

NumPy/Python version information:

Python is 3.9.1, debug version, with assertions NumPy is 1.20.0, but these leaks were present on 1.19.x as well. I haven’t checked previous versions, because that’s when pybind11 incorporated valgrind in its CI.

[seberg]

OK, I had another look. The reason that I couldn’t reproduce it at first is that it is related to cython’s CYTHON_COMPILING_IN_LIMITED_API (I assume that the debug build disables it – pypy build would also), not compiling it with the that flag, will ensure that valgrind cannot consider it “definitely lost” because the module is never “cleaned up” and a pointer will be kept until the end. On the up-side: That proofs that the leak is really just one tuple, and it doesn’t really matter much.

Now I find it a bit strange that is only one tuple is lost per file, and I do not really see where there might be a DECREF missing (unless we actually have an import error that gets eaten later). I am a bit wondering if Pythons tuple free-list could be involved, but I expect it should be cleared out correctly (and even if not, should probably not show up as lost memory in valgrind.)

[YannickJadoul]

Thanks for confirming. We’ll stick to the current suppression files, then, and hopefully in some future, we try without and find a beautiful world without suppression files 😉