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SultanOrazbayev opened this issue Jun 21, 2023 · 3 comments · Fixed by #464
Closed

bug: Fatal Python error: Segmentation fault #463

SultanOrazbayev opened this issue Jun 21, 2023 · 3 comments · Fixed by #464

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@SultanOrazbayev
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I am getting errors when trying to pytest the main branch. The traceback is in the details below:

(graphblas-dev) mymac@Mys-Mac-mini grgr % pytest graphblas
Running tests with "suitesparse" backend, blocking=True, record=False, mapnumpy=False, runslow=False
============================================ test session starts ============================================
platform darwin -- Python 3.11.4, pytest-7.3.2, pluggy-1.0.0
rootdir: /Users/mymac/grgr
configfile: setup.cfg
plugins: cov-4.1.0
collected 684 items                                                                                         

graphblas/tests/test_core.py .....                                                                    [  0%]
graphblas/tests/test_descriptor.py ..                                                                 [  1%]
graphblas/tests/test_dtype.py ..................                                                      [  3%]
graphblas/tests/test_formatting.py FFFFFFFFF.FFFFFFFFF..........FFFFFF......FF....F.FF                [ 11%]
graphblas/tests/test_infix.py ..........                                                              [ 12%]
graphblas/tests/test_io.py ......F...sss                                                              [ 14%]
graphblas/tests/test_mask.py ......                                                                   [ 15%]
graphblas/tests/test_matrix.py ...............................................s.s..............ss.... [ 25%]
...FFFF............F.....................s..ss.....FF......F...F...                                   [ 35%]
graphblas/tests/test_numpyops.py .sssss                                                               [ 36%]
graphblas/tests/test_op.py .............Fssss.....sssss..s.s.s.......                                 [ 42%]
graphblas/tests/test_operator_types.py ....                                                           [ 42%]
graphblas/tests/test_pickle.py ssss.                                                                  [ 43%]
graphblas/tests/test_prefix_scan.py ................................................................. [ 53%]
..................................................................................................... [ 67%]
........................................                                                              [ 73%]
graphblas/tests/test_pygraphblas.py sss                                                               [ 74%]
graphblas/tests/test_recorder.py ........                                                             [ 75%]
graphblas/tests/test_resolving.py ...............                                                     [ 77%]
graphblas/tests/test_scalar.py ...........s..F..................                                      [ 82%]
graphblas/tests/test_ss_utils.py FFFFFatal Python error: Segmentation fault

Current thread 0x00000001f6e45e00 (most recent call first):
  File "/Users/mymac/grgr/graphblas/ss/_core.py", line 227 in __getitem__
  File "/Users/mymac/grgr/graphblas/tests/test_ss_utils.py", line 189 in test_about
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/python.py", line 194 in pytest_pyfunc_call
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/python.py", line 1799 in runtest
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 169 in pytest_runtest_call
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 262 in <lambda>
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 341 in from_call
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 261 in call_runtest_hook
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 222 in call_and_report
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 133 in runtestprotocol
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/runner.py", line 114 in pytest_runtest_protocol
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/main.py", line 348 in pytest_runtestloop
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/main.py", line 323 in _main
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/main.py", line 269 in wrap_session
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/main.py", line 316 in pytest_cmdline_main
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/config/__init__.py", line 166 in main
  File "/Users/mymac/miniconda3/envs/graphblas-dev/lib/python3.11/site-packages/_pytest/config/__init__.py", line 189 in console_main
  File "/Users/mymac/miniconda3/envs/graphblas-dev/bin/pytest", line 10 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, suitesparse_graphblas.utils, _cffi_backend, yaml._yaml, scipy._lib._ccallback_c, numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, numba._dispatcher, numba.core.runtime._nrt_python, numba.np.ufunc._internal, numba.experimental.jitclass._box, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg._cythonized_array_utils, scipy.linalg._flinalg, scipy.linalg._solve_toeplitz, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_lapack, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, 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, pandas._libs.hashing, pandas._libs.tslib, pandas._libs.ops, pandas._libs.arrays, pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, pandas._libs.index, pandas._libs.internals, pandas._libs.join, pandas._libs.writers, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.testing, pandas._libs.parsers, pandas._libs.json, numpy.linalg.lapack_lite, scipy.io.matlab._mio_utils, scipy.io.matlab._streams, scipy.io.matlab._mio5_utils (total: 92)
zsh: segmentation fault  pytest graphblas

I am not sure if it's related or not, but this was in a new environment and when installing the python-graphblas locally the version number seemed odd (points to 2022.10). Could this be something specific to my machine/incorrect environment setup?

(graphblas-dev) mymac@Mys-Mac-mini grgr % pip install -e . --no-deps
Obtaining file:///Users/mymac/grgr
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
Building wheels for collected packages: python-graphblas
  Building editable for python-graphblas (pyproject.toml) ... done
  Created wheel for python-graphblas: filename=python_graphblas-2022.10.1+23.g944d075-0.editable-py3-none-any.whl size=10787 sha256=f4d3aba7a797bf1346309bb0e01cbb0667b46d332561c4cc1f2faebfb296398e
  Stored in directory: /private/var/folders/v6/8sdq1_2s7gb3yppns266v4gw0000gn/T/pip-ephem-wheel-cache-9tefmp3f/wheels/17/c5/da/31eae62840467c9a2b0218149aa40c4b2b0b67dcfbf41869f5
Successfully built python-graphblas
Installing collected packages: python-graphblas
Successfully installed python-graphblas-2022.10.1+23.g944d075
@eriknw eriknw mentioned this issue Jun 21, 2023
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@SultanOrazbayev
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SultanOrazbayev commented Jun 21, 2023 •
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I just redid everything from scratch (deleting old environments/files) and cloned the repo. Now the pip install gets the recent python-graphblas version (no longer the old 2022.10 one). I also don't get the segfaults now on testing.

@eriknw
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eriknw commented Jun 22, 2023

Oops. #464 didn't actually close this issue; it actually fixed CI errors seen in #462.

Nevertheless, it looks like we can close this. If you encounter this issue again, please re-open. I was having difficulty with PyPI, coveralls, etc. today/yesterday, so maybe the internet was just borked temporarily?

@SultanOrazbayev
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Yes, this is definitely closed now.

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Fix testing fix_test_suitesparse_graphblas eriknw/grblas
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@eriknw @SultanOrazbayev