Segmentation Fault (Error 139) When Running UMAP Transform

[LiorKrengel]

I encounter a segmentation fault (error 139) when running UMAP transform using:
umap-learn: 0.5.6
numba: 0.59.1
scikit-learn: 1.4.2
numpy: 1.26.4
scipy: 1.13.0
llvmlite: 0.42.0
python: 3.12.0
The issue arises specifically when applying the transform method of UMAP within a scikit-learn Pipeline.

Code to Reproduce:

if len(X) <= max_train_size:
X_train, y_train = X, y
else:
X_train, _, y_train, _ = train_test_split(X, y, random_state=1, train_size=max_train_size, stratify=y)
# Create transformer pipelie:
pipe = Pipeline([
('scaler', StandardScaler(with_mean=False)),
('reducer', UMAP(random_state=1, n_components=n_components, n_jobs=1, verbose=True, metric='cosine')),
])
# Fit transformer on train data and then transform all the data:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
logging.info('\tFitting UMAP pipeline')
pipe.fit(X_train, y_train)
logging.info('\tApplying UMAP to reduce dimensionality')
X_reduced = pipe.transform(X)

Error Trace:
The process fails with the following trace:

2024-06-16 11:13:27 2024-06-16 08:13:27,473 - INFO ::: Applying UMAP to reduce dimensionality
2024-06-16 11:13:48 *** signal 11
2024-06-16 11:13:48 Register dump:
2024-06-16 11:13:48
2024-06-16 11:13:48 RAX: fffffffffffffff9 RBX: 00007fc898e01050 RCX: fffffffffffffffa
2024-06-16 11:13:48 RDX: 0000000000000001 RSI: 00007fff5c95aff0 RDI: 0000000014d8c6f0
2024-06-16 11:13:48 RBP: 00007fc8669f9000 R8 : 000000000000000e R9 : 0000000000000004
2024-06-16 11:13:48 R10: 0000000000000004 R11: 0000000000000001 R12: 0000000009d44940
2024-06-16 11:13:48 R13: 00007fc8669f9000 R14: 0000000014d8c6f0 R15: 0000000000000007
2024-06-16 11:13:48 RSP: 00007fff5c95aea0
2024-06-16 11:13:48
2024-06-16 11:13:48 RIP: 00007fc86b03d0a4 EFLAGS: 00010213
2024-06-16 11:13:48
2024-06-16 11:13:48 CS: 0033 FS: 0000 GS: 0000
2024-06-16 11:13:48
2024-06-16 11:13:48 Trap: 0000000e Error: 00000004 OldMask: 00000000 CR2: 669f8ffc
2024-06-16 11:13:48
2024-06-16 11:13:48 FPUCW: 0000037f FPUSW: 00000020 TAG: 00007fc8
2024-06-16 11:13:48 RIP: b1bb3af9 RDP: 00000000
2024-06-16 11:13:48
2024-06-16 11:13:48 ST(0) 0000 0000000000000000 ST(1) 0000 0000000000000000
2024-06-16 11:13:48 ST(2) 0000 0000000000000000 ST(3) ffff 8000000000000000
2024-06-16 11:13:48 ST(4) ffff 8000000000000000 ST(5) 0000 0000000000000000
2024-06-16 11:13:48 ST(6) ffff 8000000000000000 ST(7) ffff ffffffffe219652c
2024-06-16 11:13:48 mxcsr: 1fa2
2024-06-16 11:13:48 XMM0: 00000000000000000000000000000000 XMM1: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM2: 00000000000000000000000000000000 XMM3: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM4: 00000000000000000000000000000000 XMM5: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM6: 00000000000000000000000000000000 XMM7: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM8: 00000000000000000000000000000000 XMM9: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM10: 00000000000000000000000000000000 XMM11: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM12: 00000000000000000000000000000000 XMM13: 00000000000000000000000000000000
2024-06-16 11:13:48 XMM14: 00000000000000000000000000000000 XMM15: 00000000000000000000000000000000
2024-06-16 11:13:48
2024-06-16 11:13:48 Backtrace:
2024-06-16 11:13:48 [0x7fc86b03d0a4]
2024-06-16 11:13:48 [0x7fc86b03a23e]
2024-06-16 11:13:48 [0x7fc86b02374e]
2024-06-16 11:13:48 [0x7fc86b024f13]
2024-06-16 11:13:48 /var/lang/lib/python3.12/site-packages/numba/_dispatcher.cpython-312-x86_64-linux-gnu.so(+0x403c)[0x7fc87196c03c]
2024-06-16 11:13:48 /var/lang/lib/python3.12/site-packages/numba/_dispatcher.cpython-312-x86_64-linux-gnu.so(+0x4382)[0x7fc87196c382]
2024-06-16 11:13:48 /var/lang/lib/libpython3.12.so.1.0(_PyObject_MakeTpCall+0x31b)[0x7fc8b43fa24b]
2024-06-16 11:13:48 /var/lang/lib/libpython3.12.so.1.0(_PyEval_EvalFrameDefault+0x6f9)[0x7fc8b4402659]
2024-06-16 11:13:48 /var/lang/lib/libpython3.12.so.1.0(+0x262108)[0x7fc8b445a108]
2024-06-16 11:13:48 /var/lang/lib/libpython3.12.so.1.0(_PyEval_EvalFrameDefault+0x59d3)[0x7fc8b4407933]
2024-06-16 11:13:48 /var/lang/lib/libpython3.12.so.1.0(PyEval_EvalCode+0x9c)[0x7fc8b44c89ac]

[dhadas]

I am facing the exact same issue. Any help on this ?