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Segmentation fault for test_krr_bob on macOS #119

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RMeli opened this issue Sep 16, 2019 · 2 comments
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Segmentation fault for test_krr_bob on macOS #119

RMeli opened this issue Sep 16, 2019 · 2 comments

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@RMeli
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RMeli commented Sep 16, 2019

The test test_krr_bob produces a segmentation fault on macOS (10.14):

================================================================================== test session starts ===================================================================================
platform darwin -- Python 3.6.9, pytest-5.1.2, py-1.8.0, pluggy-0.13.0 -- /Users/rmeli/miniconda3/envs/qml/bin/python
cachedir: .pytest_cache
rootdir: /Users/rmeli/Documents/git/software/qml
collected 90 items                                                                                                                                                                       

test/test_acsf.py::test_acsf_1 PASSED                                                                                                                                              [  1%]
test/test_acsf.py::test_acsf_2 PASSED                                                                                                                                              [  2%]
test/test_acsf_linear_angles.py::test_fchl_acsf PASSED                                                                                                                             [  3%]
test/test_acsf_linear_angles.py::test_acsf PASSED                                                                                                                                  [  4%]
test/test_arad.py::test_arad PASSED                                                                                                                                                [  5%]
test/test_armp.py::test_set_representation PASSED                                                                                                                                  [  6%]
test/test_armp.py::test_set_properties PASSED                                                                                                                                      [  7%]
test/test_armp.py::test_set_descriptor PASSED                                                                                                                                      [  8%]
test/test_armp.py::test_fit_1 PASSED                                                                                                                                               [ 10%]
test/test_armp.py::test_fit_2 PASSED                                                                                                                                               [ 11%]
test/test_armp.py::test_fit_3 PASSED                                                                                                                                               [ 12%]
test/test_armp.py::test_fit_4 PASSED                                                                                                                                               [ 13%]
test/test_armp.py::test_score_3 PASSED                                                                                                                                             [ 14%]
test/test_armp.py::test_predict_3 PASSED                                                                                                                                           [ 15%]
test/test_armp.py::test_predict_fromxyz PASSED                                                                                                                                     [ 16%]
test/test_armp.py::test_retraining PASSED                                                                                                                                          [ 17%]
test/test_compound.py::test_compound PASSED                                                                                                                                        [ 18%]
test/test_distance.py::test_manhattan PASSED                                                                                                                                       [ 20%]
test/test_distance.py::test_l2 PASSED                                                                                                                                              [ 21%]
test/test_distance.py::test_p PASSED                                                                                                                                               [ 22%]
test/test_energy_krr_atomic_cmat.py::test_krr_gaussian_local_cmat PASSED                                                                                                           [ 23%]
test/test_energy_krr_atomic_cmat.py::test_krr_laplacian_local_cmat PASSED                                                                                                          [ 24%]
test/test_energy_krr_bob.py::test_krr_bob Fatal Python error: Segmentation fault

Thread 0x000070000e7bf000 (most recent call first):
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/threading.py", line 295 in wait
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/queue.py", line 164 in get
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/tensorflow/python/summary/writer/event_file_writer.py", line 159 in run
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/threading.py", line 916 in _bootstrap_inner
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/threading.py", line 884 in _bootstrap

Current thread 0x0000000113a955c0 (most recent call first):
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/qml/representations/representations.py", line 314 in generate_bob
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/qml/utils/compound.py", line 249 in generate_bob
  File "/Users/rmeli/Documents/git/software/qml/test/test_energy_krr_bob.py", line 74 in test_krr_bob
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/python.py", line 170 in pytest_pyfunc_call
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/python.py", line 1423 in runtest
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 117 in pytest_runtest_call
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 192 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 220 in from_call
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 192 in call_runtest_hook
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 167 in call_and_report
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 87 in runtestprotocol
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/runner.py", line 72 in pytest_runtest_protocol
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 256 in pytest_runtestloop
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 235 in _main
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 191 in wrap_session
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/main.py", line 228 in pytest_cmdline_main
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/callers.py", line 187 in _multicall
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 86 in <lambda>
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/manager.py", line 92 in _hookexec
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/pluggy/hooks.py", line 286 in __call__
  File "/Users/rmeli/miniconda3/envs/qml/lib/python3.6/site-packages/_pytest/config/__init__.py", line 78 in main
  File "/Users/rmeli/miniconda3/envs/qml/bin/pytest", line 10 in <module>
[1]    18142 segmentation fault  pytest -v

The segmentation fault comes from subroutine fgenerate_bob in frepresentations.f90 when called by def generate_bob in representations.py.

Installation

Installation on develop branch.

conda create -n qml python=3.6 ipython
conda activate qml
pip install numpy scipy pandoc ase pandas scikit-learn tensorflow pytest
python setup.py build
python setup.py install
@RMeli RMeli mentioned this issue Sep 16, 2019
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@andersx
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andersx commented Sep 16, 2019

Thanks for the report, I'll investigate the reason for the segfault!

Also, thanks for the PR! Really useful addition for the build matrix!

@andersx
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andersx commented Sep 19, 2019

I am trying to find someone with a mac that I can borrow in order to get this fixed, likely won't happen this week, unfortunately.

cstein added a commit to cstein/qml that referenced this issue Nov 12, 2019
@cstein
Fixes qmlcode#119
2db7a2a 
When declaring a variable as out in fortran the value
is not defined. The function get_indices used the old
value and thus redeclared as inout
andersx pushed a commit that referenced this issue Nov 13, 2019
@cstein @andersx
Fixes #119 (#123)
18f4e9b 
When declaring a variable as out in fortran the value
is not defined. The function get_indices used the old
value and thus redeclared as inout
@RMeli RMeli mentioned this issue Aug 2, 2021
Open
@RMeli RMeli closed this as not planned Won't fix, can't repro, duplicate, stale Aug 14, 2023
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@andersx @RMeli