tests: racoon dataset generation is flaky on arm mac

Open ap-- opened this issue 9 months ago • 1 comments
The skimage.segmentation.slic call segfaults occasionally on arm64 mac
Mar 17 '25 14:03 ap--
Example of the segfault when running the tests
Fatal Python error: Segmentation fault

Thread 0x000000030704f000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x0000000306043000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x0000000305037000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x000000030402b000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x000000030301f000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x0000000301007000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x000000016ffe3000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x000000016efd7000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Thread 0x000000016dfcb000 (most recent call first):
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/concurrent/futures/thread.py", line 89 in _worker
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1012 in run
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1075 in _bootstrap_inner
  File "/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/threading.py", line 1032 in _bootstrap

Current thread 0x00000001faa38240 (most recent call first):
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/skimage/color/colorconv.py", line 857 in rgb2xyz
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/skimage/_shared/utils.py", line 445 in fixed_func
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/skimage/color/colorconv.py", line 1280 in rgb2lab
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/skimage/_shared/utils.py", line 445 in fixed_func
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/skimage/segmentation/slic_superpixels.py", line 315 in slic
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/skimage/_shared/utils.py", line 445 in fixed_func
  File "/Users/benjaminr/Documents/GitHub/spatialdata/src/spatialdata/datasets.py", line 94 in raccoon
  File "/Users/benjaminr/Documents/GitHub/spatialdata/src/spatialdata/datasets.py", line 79 in raccoon
  File "/Users/benjaminr/Documents/GitHub/spatialdata/tests/datasets/test_datasets.py", line 21 in test_datasets
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/python.py", line 159 in pytest_pyfunc_call
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/python.py", line 1627 in runtest
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 174 in pytest_runtest_call
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 242 in <lambda>
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 341 in from_call
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 241 in call_and_report
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 132 in runtestprotocol
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/main.py", line 362 in pytest_runtestloop
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/main.py", line 337 in _main
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/main.py", line 283 in wrap_session
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/main.py", line 330 in pytest_cmdline_main
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Users/benjaminr/Documents/GitHub/spatialdata/.venv/lib/python3.12/site-packages/_pytest/config/__init__.py", line 175 in main
  File "/Users/benjaminr/.vscode/extensions/ms-python.python-2025.3.2025031001-darwin-arm64/python_files/vscode_pytest/run_pytest_script.py", line 64 in <module>

Extension modules: yaml._yaml, markupsafe._speedups, numpy._core._multiarray_umath, numpy.linalg._umath_linalg, psutil._psutil_osx, psutil._psutil_posix, scipy._lib._ccallback_c, charset_normalizer.md, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg._matfuncs_expm, scipy.linalg._linalg_pythran, scipy.linalg.cython_blas, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.fftpack.convolve, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.typing.builtins.itertools, numba.cpython.builtins.math, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, pyarrow.lib, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, shapely.lib, shapely._geos, shapely._geometry_helpers, pyproj._compat, pyproj._context, pyproj._network, pyproj._version, pyproj._geod, pyproj.list, pyproj._crs, pyproj.database, pyproj._transformer, pyproj._sync, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.utils, h5py.h5t, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5r, h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5o, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5l, h5py._selector, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, msgpack._cmsgpack, numcodecs.jenkins, numcodecs.vlen, numcodecs.fletcher32, torch._C, torch._C._dynamo.autograd_compiler, torch._C._dynamo.eval_frame, torch._C._dynamo.guards, torch._C._dynamo.utils, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, scipy.ndimage._nd_image, scipy.ndimage._rank_filter_1d, _ni_label, scipy.ndimage._ni_label, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, skimage.measure._moments_cy, skimage.measure._find_contours_cy, skimage.measure._marching_cubes_lewiner_cy, numba.mviewbuf, numba.core.typing.cmathdecl.cmath, PIL._imaging, numba.types.itertools, pyarrow._fs, pyarrow._azurefs, pyarrow._hdfs, pyarrow._gcsfs, pyarrow._s3fs, pyarrow._acero, pyarrow._csv, pyarrow._json, pyarrow._substrait, pyarrow._dataset, pyarrow._dataset_orc, pyarrow._parquet, pyarrow._parquet_encryption, pyarrow._dataset_parquet_encryption, pyarrow._dataset_parquet, requests.packages.charset_normalizer.md, requests.packages.chardet.md, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._cython_nnls, scipy.linalg._decomp_interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, scipy.interpolate._dierckx, scipy.interpolate._ppoly, scipy.interpolate._interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.interpolate._bspl, skimage.measure._ccomp, skimage.segmentation._felzenszwalb_cy, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, skimage.segmentation._slic, skimage.segmentation._quickshift_cy, skimage.morphology._misc_cy, _skeletonize_lee_cy, skimage.morphology._skeletonize_lee_cy, skimage.morphology._skeletonize_various_cy, skimage._shared.geometry, skimage.measure._pnpoly, skimage.morphology._convex_hull, skimage.morphology._grayreconstruct, skimage.morphology._extrema_cy, skimage.morphology._flood_fill_cy, skimage.morphology._max_tree, skimage.segmentation._watershed_cy, skimage.transform._warps_cy, tornado.speedups, _cffi_backend, numba.core.typing.mathdecl.math, numba.cpython.hashing.math, numba.cpython.hashing.sys, numba.cpython.numbers.math, numba.np.arraymath.math, numba.cpython.mathimpl.math, numba.cpython.mathimpl.sys, PyQt5.QtCore, PIL._imagingmath (total: 248)
/opt/homebrew/Cellar/[email protected]/3.12.7_1/Frameworks/Python.framework/Versions/3.12/lib/python3.12/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '
Finished running tests!
Mar 17 '25 14:03 berombau