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Segfault on test suite with 'clifford/test/test_cga.py::test_round_from_center_radius_init' for version 'v1.3.0' on OSX #376

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esc opened this issue Nov 13, 2020 · 18 comments
Open

Segfault on test suite with 'clifford/test/test_cga.py::test_round_from_center_radius_init' for version 'v1.3.0' on OSX #376

esc opened this issue Nov 13, 2020 · 18 comments

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@esc
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esc commented Nov 13, 2020

I am on OSX Version 10.15.7 -- Steps to reproduce:

# Assuming we are inside a clone of the clifford repo
$ git checkout v1.3.0
Note: checking out 'v1.3.1'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 2da66d3243 Merge pull request #324 from eric-wieser/release-1.3.1

$ git status
HEAD detached at v1.3.1
nothing to commit, working tree clean

# Assuming miniconda is activate and conda exists on the path
$ conda create -n clifford "python<=3.8" ipython numba numpy scipy pip h5py pytest conda-forge::sparse
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/esc/miniconda3/envs/clifford

  added / updated specs:
    - conda-forge::sparse
    - h5py
    - ipython
    - numba
    - numpy
    - pip
    - pytest
    - python[version='<=3.8']
    - scipy


The following NEW packages will be INSTALLED:

  appnope            pkgs/main/osx-64::appnope-0.1.0-py37_0
  attrs              pkgs/main/noarch::attrs-20.3.0-pyhd3eb1b0_0
  blas               pkgs/main/osx-64::blas-1.0-mkl
  ca-certificates    pkgs/main/osx-64::ca-certificates-2020.10.14-0
  certifi            pkgs/main/noarch::certifi-2020.6.20-pyhd3eb1b0_3
  decorator          pkgs/main/noarch::decorator-4.4.2-py_0
  h5py               pkgs/main/osx-64::h5py-2.10.0-py37h0601b69_1
  hdf5               pkgs/main/osx-64::hdf5-1.10.6-hdbbcd12_0
  importlib-metadata pkgs/main/noarch::importlib-metadata-2.0.0-py_1
  importlib_metadata pkgs/main/noarch::importlib_metadata-2.0.0-1
  iniconfig          pkgs/main/noarch::iniconfig-1.1.1-py_0
  intel-openmp       pkgs/main/osx-64::intel-openmp-2019.4-233
  ipython            conda-forge/osx-64::ipython-5.8.0-py37_1
  ipython_genutils   pkgs/main/osx-64::ipython_genutils-0.2.0-py37_0
  libcxx             pkgs/main/osx-64::libcxx-10.0.0-1
  libedit            pkgs/main/osx-64::libedit-3.1.20191231-h1de35cc_1
  libffi             pkgs/main/osx-64::libffi-3.3-hb1e8313_2
  libgfortran        pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
  libllvm10          pkgs/main/osx-64::libllvm10-10.0.1-h76017ad_5
  llvm-openmp        pkgs/main/osx-64::llvm-openmp-10.0.0-h28b9765_0
  llvmlite           pkgs/main/osx-64::llvmlite-0.34.0-py37h739e7dc_4
  mkl                pkgs/main/osx-64::mkl-2019.4-233
  mkl-service        pkgs/main/osx-64::mkl-service-2.3.0-py37hfbe908c_0
  mkl_fft            pkgs/main/osx-64::mkl_fft-1.2.0-py37hc64f4ea_0
  mkl_random         pkgs/main/osx-64::mkl_random-1.1.1-py37h959d312_0
  more-itertools     pkgs/main/noarch::more-itertools-8.6.0-pyhd3eb1b0_0
  ncurses            pkgs/main/osx-64::ncurses-6.2-h0a44026_1
  numba              pkgs/main/osx-64::numba-0.51.2-py37h959d312_1
  numpy              pkgs/main/osx-64::numpy-1.19.2-py37h456fd55_0
  numpy-base         pkgs/main/osx-64::numpy-base-1.19.2-py37hcfb5961_0
  openssl            pkgs/main/osx-64::openssl-1.1.1h-haf1e3a3_0
  packaging          pkgs/main/noarch::packaging-20.4-py_0
  pexpect            pkgs/main/osx-64::pexpect-4.8.0-py37_0
  pickleshare        pkgs/main/osx-64::pickleshare-0.7.5-py37_0
  pip                pkgs/main/osx-64::pip-20.2.4-py37hecd8cb5_0
  pluggy             pkgs/main/osx-64::pluggy-0.13.1-py37_0
  prompt_toolkit     conda-forge/noarch::prompt_toolkit-1.0.15-py_1
  ptyprocess         pkgs/main/osx-64::ptyprocess-0.6.0-py37_0
  py                 pkgs/main/noarch::py-1.9.0-py_0
  pygments           pkgs/main/noarch::pygments-2.7.2-pyhd3eb1b0_0
  pyparsing          pkgs/main/noarch::pyparsing-2.4.7-py_0
  pytest             pkgs/main/osx-64::pytest-6.1.1-py37_0
  python             pkgs/main/osx-64::python-3.7.9-h26836e1_0
  readline           pkgs/main/osx-64::readline-8.0-h1de35cc_0
  scipy              pkgs/main/osx-64::scipy-1.5.2-py37h912ce22_0
  setuptools         pkgs/main/osx-64::setuptools-50.3.1-py37hecd8cb5_1
  simplegeneric      pkgs/main/osx-64::simplegeneric-0.8.1-py37_2
  six                pkgs/main/osx-64::six-1.15.0-py37hecd8cb5_0
  sparse             conda-forge/noarch::sparse-0.11.2-py_0
  sqlite             pkgs/main/osx-64::sqlite-3.33.0-hffcf06c_0
  tk                 pkgs/main/osx-64::tk-8.6.10-hb0a8c7a_0
  toml               pkgs/main/noarch::toml-0.10.1-py_0
  traitlets          pkgs/main/noarch::traitlets-5.0.5-py_0
  wcwidth            pkgs/main/noarch::wcwidth-0.2.5-py_0
  wheel              pkgs/main/noarch::wheel-0.35.1-py_0
  xz                 pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
  zipp               pkgs/main/noarch::zipp-3.4.0-pyhd3eb1b0_0
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate clifford
#
# To deactivate an active environment, use
#
#     $ conda deactivate

$ conda activate clifford

$ python setup.py install
running install
running bdist_egg
running egg_info
creating clifford.egg-info
writing clifford.egg-info/PKG-INFO
writing dependency_links to clifford.egg-info/dependency_links.txt
writing requirements to clifford.egg-info/requires.txt
writing top-level names to clifford.egg-info/top_level.txt
writing manifest file 'clifford.egg-info/SOURCES.txt'
reading manifest file 'clifford.egg-info/SOURCES.txt'
writing manifest file 'clifford.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/clifford
copying clifford/_blademap.py -> build/lib/clifford
copying clifford/_layout_helpers.py -> build/lib/clifford
copying clifford/_version.py -> build/lib/clifford
copying clifford/g4.py -> build/lib/clifford
copying clifford/transformations.py -> build/lib/clifford
copying clifford/sta.py -> build/lib/clifford
copying clifford/dg3c.py -> build/lib/clifford
copying clifford/io.py -> build/lib/clifford
copying clifford/dpga.py -> build/lib/clifford
copying clifford/operator.py -> build/lib/clifford
copying clifford/__init__.py -> build/lib/clifford
copying clifford/g3_1.py -> build/lib/clifford
copying clifford/_numba_utils.py -> build/lib/clifford
copying clifford/code_gen.py -> build/lib/clifford
copying clifford/_parser.py -> build/lib/clifford
copying clifford/g3c.py -> build/lib/clifford
copying clifford/_settings.py -> build/lib/clifford
copying clifford/g2c.py -> build/lib/clifford
copying clifford/pga.py -> build/lib/clifford
copying clifford/_bit_helpers.py -> build/lib/clifford
copying clifford/caching.py -> build/lib/clifford
copying clifford/_multivector.py -> build/lib/clifford
copying clifford/_conformal_layout.py -> build/lib/clifford
copying clifford/_mvarray.py -> build/lib/clifford
copying clifford/_layout.py -> build/lib/clifford
copying clifford/gac.py -> build/lib/clifford
copying clifford/_frame.py -> build/lib/clifford
copying clifford/g3.py -> build/lib/clifford
copying clifford/cga.py -> build/lib/clifford
copying clifford/g2.py -> build/lib/clifford
creating build/lib/clifford/tools
copying clifford/tools/point_processing.py -> build/lib/clifford/tools
copying clifford/tools/classify.py -> build/lib/clifford/tools
copying clifford/tools/__init__.py -> build/lib/clifford/tools
creating build/lib/clifford/test
copying clifford/test/test_parser.py -> build/lib/clifford/test
copying clifford/test/test_g3c_tools.py -> build/lib/clifford/test
copying clifford/test/test_clifford.py -> build/lib/clifford/test
copying clifford/test/test_dg3c.py -> build/lib/clifford/test
copying clifford/test/__init__.py -> build/lib/clifford/test
copying clifford/test/test_dpga.py -> build/lib/clifford/test
copying clifford/test/test_degenerate.py -> build/lib/clifford/test
copying clifford/test/test_io.py -> build/lib/clifford/test
copying clifford/test/test_g3c_CUDA.py -> build/lib/clifford/test
copying clifford/test/test_cga.py -> build/lib/clifford/test
copying clifford/test/test_algebra_initialisation.py -> build/lib/clifford/test
copying clifford/test/test_transformations.py -> build/lib/clifford/test
copying clifford/test/test_aliases.py -> build/lib/clifford/test
copying clifford/test/test_tools_classify.py -> build/lib/clifford/test
copying clifford/test/test_bit_helpers.py -> build/lib/clifford/test
copying clifford/test/test_layout.py -> build/lib/clifford/test
copying clifford/test/test_layout_helpers.py -> build/lib/clifford/test
copying clifford/test/test_tools.py -> build/lib/clifford/test
creating build/lib/clifford/tools/g3c
copying clifford/tools/g3c/rotor_estimation.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/GAOnline.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/cost_functions.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/object_fitting.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/model_matching.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/__init__.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/cuda_products.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/cuda.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/scene_simplification.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/rotor_parameterisation.py -> build/lib/clifford/tools/g3c
copying clifford/tools/g3c/object_clustering.py -> build/lib/clifford/tools/g3c
creating build/lib/clifford/tools/g3
copying clifford/tools/g3/__init__.py -> build/lib/clifford/tools/g3
creating build/bdist.macosx-10.9-x86_64
creating build/bdist.macosx-10.9-x86_64/egg
creating build/bdist.macosx-10.9-x86_64/egg/clifford
creating build/bdist.macosx-10.9-x86_64/egg/clifford/tools
copying build/lib/clifford/tools/point_processing.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools
copying build/lib/clifford/tools/classify.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools
copying build/lib/clifford/tools/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools
creating build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/rotor_estimation.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/GAOnline.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/cost_functions.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/object_fitting.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/model_matching.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/cuda_products.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/cuda.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/scene_simplification.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/rotor_parameterisation.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
copying build/lib/clifford/tools/g3c/object_clustering.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c
creating build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3
copying build/lib/clifford/tools/g3/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3
copying build/lib/clifford/_blademap.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_layout_helpers.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
creating build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_parser.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_g3c_tools.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_clifford.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_dg3c.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_dpga.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_degenerate.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_io.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_g3c_CUDA.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_cga.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_algebra_initialisation.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_transformations.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_aliases.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_tools_classify.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_bit_helpers.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_layout.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_layout_helpers.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/test/test_tools.py -> build/bdist.macosx-10.9-x86_64/egg/clifford/test
copying build/lib/clifford/_version.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/g4.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/transformations.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/sta.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/dg3c.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/io.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/dpga.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/operator.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/g3_1.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_numba_utils.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/code_gen.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_parser.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/g3c.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_settings.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/g2c.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/pga.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_bit_helpers.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/caching.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_multivector.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_conformal_layout.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_mvarray.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_layout.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/gac.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/_frame.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/g3.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/cga.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
copying build/lib/clifford/g2.py -> build/bdist.macosx-10.9-x86_64/egg/clifford
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/point_processing.py to point_processing.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/classify.py to classify.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/rotor_estimation.py to rotor_estimation.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/GAOnline.py to GAOnline.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/cost_functions.py to cost_functions.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/object_fitting.py to object_fitting.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/model_matching.py to model_matching.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/cuda_products.py to cuda_products.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/cuda.py to cuda.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/scene_simplification.py to scene_simplification.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/rotor_parameterisation.py to rotor_parameterisation.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3c/object_clustering.py to object_clustering.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/tools/g3/__init__.py to __init__.cpython-37.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/clifford/_blademap.py to _blademap.cpython-37.pyc
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creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying clifford.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
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clifford.test.__pycache__.__init__.cpython-37: module references __file__
creating dist
creating 'dist/clifford-1.3.1-py3.7.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it
removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)
Processing clifford-1.3.1-py3.7.egg
creating /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages/clifford-1.3.1-py3.7.egg
Extracting clifford-1.3.1-py3.7.egg to /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Adding clifford 1.3.1 to easy-install.pth file

Installed /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages/clifford-1.3.1-py3.7.egg
Processing dependencies for clifford==1.3.1
Searching for sparse==0.11.2
Best match: sparse 0.11.2
Adding sparse 0.11.2 to easy-install.pth file

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Searching for h5py==2.10.0
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Adding h5py 2.10.0 to easy-install.pth file

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Searching for numba==0.51.2
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Adding numba 0.51.2 to easy-install.pth file

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Searching for scipy==1.5.2
Best match: scipy 1.5.2
Adding scipy 1.5.2 to easy-install.pth file

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Searching for numpy==1.19.2
Best match: numpy 1.19.2
Adding numpy 1.19.2 to easy-install.pth file
Installing f2py script to /Users/esc/miniconda3/envs/clifford/bin
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Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
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Adding six 1.15.0 to easy-install.pth file

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
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Adding setuptools 50.3.1.post20201107 to easy-install.pth file
Installing easy_install script to /Users/esc/miniconda3/envs/clifford/bin

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Searching for llvmlite==0.34.0
Best match: llvmlite 0.34.0
Adding llvmlite 0.34.0 to easy-install.pth file

Using /Users/esc/miniconda3/envs/clifford/lib/python3.7/site-packages
Finished processing dependencies for clifford==1.3.1

$ pytest -v clifford/test/test_cga.py::test_round_from_center_radius_init
========================================================================= test session starts =========================================================================
platform darwin -- Python 3.7.9, pytest-6.1.1, py-1.9.0, pluggy-0.13.1 -- /Users/esc/miniconda3/envs/clifford/bin/python
cachedir: .pytest_cache
rootdir: /Users/esc/git/clifford, configfile: setup.cfg
collected 1 item

clifford/test/test_cga.py::test_round_from_center_radius_init [1]    59113 abort (core dumped)  pytest -v clifford/test/test_cga.py::test_round_from_center_radius_init
@esc esc changed the title Segfault on test suite with 'clifford/test/test_cga.py::test_round_from_center_radius_init' v1.3.0 on OSX Segfault on test suite with 'clifford/test/test_cga.py::test_round_from_center_radius_init' for version 'v1.3.0' on OSX Nov 13, 2020
@eric-wieser
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Does this happen every time? If you, can you check if master suffers the same problem?

@esc
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esc commented Nov 13, 2020

Happens every time yes, is fine on master.

@eric-wieser
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Test in question is:

clifford/clifford/test/test_cga.py

Lines 84 to 92 in 2da66d3

@pytest.mark.xfail(raises=AssertionError, reason='gh-184')
def test_round_from_center_radius_init(cga):
blades = cga.layout.blades
e1 = blades['e1']
e2 = blades['e2']
c = cga.round((3*e1+4*e2, 5))
npt.assert_almost_equal(c.center_down, 3*e1+4*e2)
npt.assert_almost_equal(c.radius, 5)

@eric-wieser
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Can you run with python fault handling enabled so that we get a traceback?

@esc
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esc commented Nov 13, 2020

@eric-wieser sure, could you point me at some documentation on how to do that?

@eric-wieser
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It looks like its supposed to be enabled by default... https://docs.pytest.org/en/stable/usage.html#fault-handler

@eric-wieser
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Using python3 -X faulthandler -m pytest instead of pytest might force it to jump into action

@esc
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esc commented Nov 13, 2020 •
edited
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Yeah, I think this didn't really get us any further:

zsh» python3 -X faulthandler -m pytest clifford/test/test_cga.py::test_round_from_center_radius_init
========================================================================= test session starts =========================================================================
platform darwin -- Python 3.7.9, pytest-6.1.1, py-1.9.0, pluggy-0.13.1
rootdir: /Users/esc/git/numba-integration-testing/clifford, configfile: setup.cfg
collected 1 item

clifford/test/test_cga.py [1]    62305 abort (core dumped)  python3 -X faulthandler -m pytest
python3 -X faulthandler -m pytest   15.51s user 7.18s system 129% cpu 17.489 total

FWIW: I also tried to use lldb but didn't get anything useful:

zsh» lldb -- python -m pytest -v clifford/test/test_cga.py::test_round_from_center_radius_init          
(lldb) target create "python"
Current executable set to 'python' (x86_64).
(lldb) settings set -- target.run-args  "-m" "pytest" "-v" "clifford/test/test_cga.py::test_round_from_center_radius_init"
(lldb) run
Process 59350 launched: '/Users/esc/miniconda3/envs/clifford/bin/python' (x86_64)
============================= test session starts ==============================
platform darwin -- Python 3.7.9, pytest-6.1.1, py-1.9.0, pluggy-0.13.1 -- /Users/esc/miniconda3/envs/clifford/bin/python
cachedir: .pytest_cache
rootdir: /Users/esc/git/clifford, configfile: setup.cfg
collected 1 item
clifford/test/test_cga.py::test_round_from_center_radius_init Process 59350 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGABRT
    frame #0: 0x00007fff69af633a
->  0x7fff69af633a: jae    0x7fff69af6344
    0x7fff69af633c: movq   %rax, %rdi
    0x7fff69af633f: jmp    0x7fff69af0629
    0x7fff69af6344: retq
Target 0: (_fblas.cpython-37m-darwin.so) stopped.

@eric-wieser
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Can you diagnose which line is failing by inserting print statements between each line of the test?

@esc
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esc commented Nov 13, 2020

So, I have some news on this. It seems like pytest was capturing the stdout/stderr. Adding the -s flag for no-capture, results in the following.

zsh» pytest -s -v clifford/test/test_cga.py::test_round_from_center_radius_init
========================================================================= test session starts =========================================================================
platform darwin -- Python 3.7.9, pytest-6.1.1, py-1.9.0, pluggy-0.13.1 -- /Users/esc/git/numba-integration-testing/miniconda3/envs/clifford/bin/python
cachedir: .pytest_cache
rootdir: /Users/esc/git/numba-integration-testing/clifford, configfile: setup.cfg
collected 1 item

clifford/test/test_cga.py::test_round_from_center_radius_init OMP: Info #270: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
the
fish
was
caught
with
Fatal Python error: Cannot recover from stack overflow.

Current thread 0x0000000112d4bdc0 (most recent call first):
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
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  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_multivector.py", line 62 in __array__
  File "/Users/esc/git/numba-integration-testing/clifford/clifford/_mvarray.py", line 19 in __new__
  ...
[3]    77832 abort (core dumped)  pytest -s -v clifford/test/test_cga.py::test_round_from_center_radius_init
pytest -s -v clifford/test/test_cga.py::test_round_from_center_radius_init  16.72s user 6.53s system 139% cpu 16.662 total

@esc
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esc commented Nov 13, 2020

This is the debugging patch which is responsible for the output lines:

diff --git i/clifford/test/test_cga.py w/clifford/test/test_cga.py
index 618e57ee0d..0fc5e6f8ac 100644
--- i/clifford/test/test_cga.py
+++ w/clifford/test/test_cga.py
@@ -83,13 +83,20 @@ def test_from_points_construction(cga, method):

 @pytest.mark.xfail(raises=AssertionError, reason='gh-184')
 def test_round_from_center_radius_init(cga):
+    print("the")
     blades = cga.layout.blades
+    print("fish")
     e1 = blades['e1']
+    print("was")
     e2 = blades['e2']
+    print("caught")

     c = cga.round((3*e1+4*e2, 5))
+    print("with")
     npt.assert_almost_equal(c.center_down, 3*e1+4*e2)
+    print("good")
     npt.assert_almost_equal(c.radius, 5)
+    print("intentions")

@esc
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esc commented Nov 13, 2020

Looks like it might be the line

npt.assert_almost_equal(c.center_down, 3*e1+4*e2)

@eric-wieser
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Thanks, that gives me plenty to work with. I wonder whether this is actually a numpy incompatibility.

@esc
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esc commented Nov 16, 2020

@eric-wieser that was a good hunch, I tried with Numpy 1.18.5 and the test did not segfault.

@eric-wieser
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I imagine this means that this reproduces on windows

@eric-wieser
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And my guess would be that the bug was fixed in clifford by a1b1ba3

@eric-wieser eric-wieser mentioned this issue Nov 16, 2020
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@eric-wieser
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Either way, thanks for the dive into the cause - I've reported a bug against numpy, which I might take a look at next time I put on my numpy hat.

@esc
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esc commented Nov 16, 2020

@eric-wieser shall we keep the issue open? I made the integration tests pass, for now:

numba/numba-integration-testing#56

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