Segmentation fault (core dumped) - Ubuntu 20.04

Configuration

Ubuntu 20.04 Conda 4.8.2 Python 3.6.10

Problem

I’m trying to install habitat api following these instructions.

Everything works until step 4, the installation and testing of habitat sim works well, no issues.

But when I try to run python examples/example.py, python examples/benchmark.py, or the code here, it just prints Segmentation fault (core dumped).

The output for python setup.py test is a bit different, but ends the same way : ` running pytest Searching for pytest-mock Best match: pytest-mock 3.1.0 Processing pytest_mock-3.1.0-py3.6.egg

Using /home/juungko/habitat/habitat-api/.eggs/pytest_mock-3.1.0-py3.6.egg running egg_info writing habitat.egg-info/PKG-INFO writing dependency_links to habitat.egg-info/dependency_links.txt writing requirements to habitat.egg-info/requires.txt writing top-level names to habitat.egg-info/top_level.txt reading manifest file ‘habitat.egg-info/SOURCES.txt’ reading manifest template ‘MANIFEST.in’ writing manifest file ‘habitat.egg-info/SOURCES.txt’ running build_ext ======================================== test session starts ========================================= platform linux – Python 3.6.10, pytest-5.4.2, py-1.8.1, pluggy-0.13.1 rootdir: /home/juungko/habitat/habitat-api, inifile: setup.cfg, testpaths: test plugins: mock-3.1.0, cov-2.9.0 collecting … Fatal Python error: Segmentation fault

Current thread 0x00007fade7658740 (most recent call first): File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/llvmlite/binding/ffi.py”, line 113 in call File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/llvmlite/binding/targets.py”, line 60 in get_host_cpu_features File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/codegen.py”, line 881 in get_host_cpu_features File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/codegen.py”, line 782 in _get_host_cpu_features File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/codegen.py”, line 846 in _customize_tm_features File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/codegen.py”, line 652 in _init File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/codegen.py”, line 645 in init File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/cpu.py”, line 47 in init File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/compiler_lock.py”, line 32 in _acquire_compile_lock File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/base.py”, line 259 in init File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/registry.py”, line 31 in _toplevel_target_context File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/utils.py”, line 332 in get File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/registry.py”, line 47 in target_context File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/dispatcher.py”, line 670 in init File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/decorators.py”, line 189 in wrapper File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/decorators.py”, line 173 in jit File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/core/decorators.py”, line 236 in njit File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/typed/typeddict.py”, line 22 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/typed/init.py”, line 1 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/numba/init.py”, line 298 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/quaternion/numba_wrapper.py”, line 11 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/quaternion/quaternion_time_series.py”, line 8 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/quaternion/init.py”, line 13 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/habitat/habitat-api/habitat/core/utils.py”, line 11 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/habitat/habitat-api/habitat/core/dataset.py”, line 31 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/habitat/habitat-api/habitat/core/simulator.py”, line 16 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/habitat/habitat-api/habitat/core/agent.py”, line 13 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/habitat/habitat-api/habitat/init.py”, line 8 in <module> File “<frozen importlib._bootstrap>”, line 219 in _call_with_frames_removed File “<frozen importlib._bootstrap_external>”, line 678 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/habitat/habitat-api/test/test_baseline_agents.py”, line 11 in <module> File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/assertion/rewrite.py”, line 152 in exec_module File “<frozen importlib._bootstrap>”, line 665 in _load_unlocked File “<frozen importlib._bootstrap>”, line 955 in _find_and_load_unlocked File “<frozen importlib._bootstrap>”, line 971 in _find_and_load File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/py/_path/local.py”, line 701 in pyimport File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/python.py”, line 511 in _importtestmodule File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/python.py”, line 443 in _getobj File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/python.py”, line 261 in obj File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/python.py”, line 459 in _inject_setup_module_fixture File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/python.py”, line 446 in collect File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/runner.py”, line 264 in <lambda> File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/runner.py”, line 244 in from_call File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/_pytest/runner.py”, line 264 in pytest_make_collect_report File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/pluggy/callers.py”, line 187 in _multicall File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/pluggy/manager.py”, line 87 in <lambda> File “/home/juungko/anaconda3/envs/habitat/lib/python3.6/site-packages/pluggy/manager.py”, line 93 in _hookexec … Segmentation fault (core dumped) ` Can you help me to get this working ?

[rpartsey]

Hi @ulysse-bouchet While setting up the habitat-sim & habitat-api (see CI instructions ), I faced up with a similar error to what you described in the Problem section above.

I run numba -s to verify that the numba was installed successfully. But Segmentation fault (core dumped) message was printed instead of information about my system capabilities.

Then I run pip uninstall numba to uninstalled numba . And installed it again but using conda conda install numba instead of pip. (I also remember that this command updated one of numba’s dependencies, but I don’t remember which exactly).

After that, I was able to successfully run all tests and build documentation pages.

[ulysse-bouchet]

Thanks. I’ll soon get a new laptop with a better GPU, it should be ok with it.