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mattragoza / LiGAN

Deep generative models of 3D grids for structure-based drug discovery
GNU General Public License v2.0
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Segmentation Fault when running tests #52

Closed zyx5256 closed 2 years ago

zyx5256 commented 2 years ago

=================================================================================== test session starts ==================================================================================== platform linux -- Python 3.7.5, pytest-7.1.2, pluggy-1.0.0 rootdir: /home/jenkins/zhuyuxiao/LiGAN_Project/LiGAN plugins: timeout-1.4.2, xdist-1.33.0, forked-1.2.0 collected 938 items

tests/test_atom_fitting.py ......................................................................................................................................................... [ 16%] ........................................ [ 20%] tests/test_atom_grids.py ........ [ 21%] tests/test_atom_structs.py . [ 21%] tests/test_atom_types.py ......................................................................FFFFFFFatal Python error: Segmentation fault

Thread 0x00007f82ab7fe700 (most recent call first):

Thread 0x00007f82abfff700 (most recent call first):

Thread 0x00007f82e8f8b700 (most recent call first):

Thread 0x00007f82e878a700 (most recent call first):

Thread 0x00007f8308a88700 (most recent call first):

Thread 0x00007f830bfff700 (most recent call first):

Thread 0x00007f8309289700 (most recent call first):

Thread 0x00007f830a9a7700 (most recent call first):

Current thread 0x00007f8595cc4740 (most recent call first): File "/home/jenkins/zhuyuxiao/LiGAN/tests/test_atom_types.py", line 124 in test_typer_coord_set File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/python.py", line 192 in pytest_pyfunc_call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_hooks.py", line 265 in call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/python.py", line 1761 in runtest File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 166 in pytest_runtest_call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_hooks.py", line 265 in call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 259 in File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 338 in from_call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 259 in call_runtest_hook File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 219 in call_and_report File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 130 in runtestprotocol File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/runner.py", line 111 in pytest_runtest_protocol File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_hooks.py", line 265 in call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/main.py", line 347 in pytest_runtestloop File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_hooks.py", line 265 in call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/main.py", line 322 in _main File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/main.py", line 268 in wrap_session File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/main.py", line 315 in pytest_cmdline_main File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/pluggy/_hooks.py", line 265 in call File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/config/init.py", line 165 in main File "/home/miniconda3/envs/zyx/lib/python3.7/site-packages/_pytest/config/init.py", line 187 in console_main File "/home/miniconda3/envs/zyx/bin/pytest", line 8 in Segmentation fault

zyx5256 commented 2 years ago

I solved this by creating a conda env using environment.yml at the beginning and follow the README instructions. Thanks