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astro-informatics / s2fft

Differentiable and accelerated spherical transforms with JAX
https://astro-informatics.github.io/s2fft
MIT License
124 stars 9 forks source link

Segmentation fault on running tests on MacOS on Python 3.9+ #212

Open matt-graham opened 2 weeks ago

matt-graham commented 2 weeks ago

Running tests/test_spherical_precompute.py::test_transform_inverse_healpix on a MacOS (arm64) runner with Python 3.9 or above generates a segmentation fault with output

Fatal Python error: Segmentation fault

Thread 0x000000017b2f3000 (most recent call first):
  <no Python frame>

Thread 0x00000002001c8f40 (most recent call first):
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/graph.py", line 769 in _engine_run_backward
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/__init__.py", line 436 in grad
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 767 in vjp_fn
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 894 in _compute_analytical_jacobian_rows
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 776 in _check_analytical_jacobian_attributes
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 1627 in _slow_gradcheck
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 1492 in _gradcheck_real_imag
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 2082 in _gradcheck_helper
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/torch/autograd/gradcheck.py", line 2053 in gradcheck
  File "/Users/runner/work/s2fft/s2fft/tests/test_spherical_precompute.py", line 111 in test_transform_inverse_healpix
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/python.py", line 159 in pytest_pyfunc_call
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/python.py", line 1627 in runtest
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/runner.py", line 174 in pytest_runtest_call
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/runner.py", line 242 in <lambda>
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/runner.py", line 341 in from_call
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/runner.py", line 241 in call_and_report
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/runner.py", line 132 in runtestprotocol
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/main.py", line 362 in pytest_runtestloop
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/main.py", line 337 in _main
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/main.py", line 283 in wrap_session
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/main.py", line 330 in pytest_cmdline_main
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_callers.py", line 103 in _multicall
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_manager.py", line 120 in _hookexec
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/pluggy/_hooks.py", line 513 in __call__
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/config/__init__.py", line 175 in main
  File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/_pytest/config/__init__.py", line 201 in console_main
  File "/Users/runner/hostedtoolcache/Python/3.12.6/arm64/bin/pytest", line 8 in <module>

Extension modules: numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, 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, astropy.io.fits._utils, astropy.io.fits.hdu.compressed._compression, healpy._healpy_sph_transform_lib, healpy._sphtools, healpy._pixelfunc, healpy._query_disc, erfa.ufunc, astropy.time._parse_times, astropy.table._column_mixins, astropy.table._np_utils, yaml._yaml, astropy.io.ascii.cparser, astropy.utils.xml._iterparser, astropy.io.votable.tablewriter, healpy._masktools, healpy._hotspots, healpy._line_integral_convolution, jaxlib.cpu_feature_guard, torch._C, torch._C._fft, torch._C._linalg, torch._C._nested, torch._C._nn, torch._C._sparse, torch._C._special, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, 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._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, pyssht.cpyssht, so3.bindings, pyssht.ducc_interface (total: 105)

This appears to be for test case with method = "torch".

jasonmcewen commented 5 days ago

Thanks for flagging this @matt-graham. Could you take a look at this @CosmoMatt?