Segmentation Fault (Core Dumped) when testing SciPy build
Hello SciPy Developers, I'm a SciPy newbie so please forgive if my question is silly. I built SciPy on my Linux machine and tried to test the build on my conda environment called scipydev. So, when I run, python3 runtests.py -v, I get a Segmentation Fault (core dumped)... Here's the related log: scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py ....... [ 54%] scipy/sparse/linalg/_isolve/tests/test_iterative.py ...........................xxxxX............................ [ 55%] scipy/sparse/linalg/_isolve/tests/test_lgmres.py ........ [ 55%] scipy/sparse/linalg/_isolve/tests/test_lsmr.py ............... [ 55%] scipy/sparse/linalg/_isolve/tests/test_lsqr.py ..... [ 55%] scipy/sparse/linalg/_isolve/tests/test_minres.py ....... [ 55%] scipy/sparse/linalg/_isolve/tests/test_utils.py . [ 55%] scipy/sparse/linalg/tests/test_expm_multiply.py ................. [ 55%] scipy/sparse/linalg/tests/test_interface.py .............. [ 55%] scipy/sparse/linalg/tests/test_matfuncs.py ............................Fatal Python error: Segmentation fault Current thread 0x00007f9bed60f740 (most recent call first): File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/linalg/_basic.py", line 223 in solve File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/_matfuncs.py", line 708 in _solve_P_Q File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/_matfuncs.py", line 672 in _expm File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/_matfuncs.py", line 590 in expm File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/tests/test_matfuncs.py", line 516 in test_pascal File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/python.py", line 192 in pytest_pyfunc_call File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/python.py", line 1718 in runtest File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 168 in pytest_runtest_call File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 261 in <lambda> File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 340 in from_call File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 260 in call_runtest_hook File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 221 in call_and_report File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 132 in runtestprotocol File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 347 in pytest_runtestloop File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 322 in _main File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 268 in wrap_session File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 315 in pytest_cmdline_main File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/config/__init__.py", line 165 in main File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/_lib/_testutils.py", line 69 in __call__ File "runtests.py", line 334 in main File "runtests.py", line 612 in <module> Segmentation fault (core dumped) What might be causing this? OS: Ubuntu 20.04.3 LTS Python: 3.8 Numpy: 1.22.2
Hi Bharath, Can you please open an issue on GitHub? And try to include a backtrace with GDB (see https://numpy.org/doc/stable/dev/development_environment.html#debugging). Including the full build log would also be good. Cheers, Ralf On Tue, Feb 15, 2022 at 6:08 PM Bharath K K <bharathkk0603@gmail.com> wrote:
Hello SciPy Developers,
I'm a SciPy newbie so please forgive if my question is silly.
I built SciPy on my Linux machine and tried to test the build on my conda environment called scipydev. So, when I run, python3 runtests.py -v, I get a Segmentation Fault (core dumped)...
Here's the related log:
scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py .......
[ 54%] scipy/sparse/linalg/_isolve/tests/test_iterative.py ...........................xxxxX............................ [ 55%] scipy/sparse/linalg/_isolve/tests/test_lgmres.py ........
[ 55%] scipy/sparse/linalg/_isolve/tests/test_lsmr.py ...............
[ 55%] scipy/sparse/linalg/_isolve/tests/test_lsqr.py .....
[ 55%] scipy/sparse/linalg/_isolve/tests/test_minres.py .......
[ 55%] scipy/sparse/linalg/_isolve/tests/test_utils.py .
[ 55%] scipy/sparse/linalg/tests/test_expm_multiply.py .................
[ 55%] scipy/sparse/linalg/tests/test_interface.py ..............
[ 55%] scipy/sparse/linalg/tests/test_matfuncs.py ............................Fatal Python error: Segmentation fault
Current thread 0x00007f9bed60f740 (most recent call first): File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/linalg/_basic.py", line 223 in solve File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/_matfuncs.py", line 708 in _solve_P_Q File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/_matfuncs.py", line 672 in _expm File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/_matfuncs.py", line 590 in expm File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/sparse/linalg/tests/test_matfuncs.py", line 516 in test_pascal File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/python.py", line 192 in pytest_pyfunc_call File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/python.py", line 1718 in runtest File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 168 in pytest_runtest_call File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 261 in <lambda> File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 340 in from_call File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 260 in call_runtest_hook File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 221 in call_and_report File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 132 in runtestprotocol File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/runner.py", line 113 in pytest_runtest_protocol File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 347 in pytest_runtestloop File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 322 in _main File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 268 in wrap_session File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/main.py", line 315 in pytest_cmdline_main File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__ File "/home/bharath/anaconda3/envs/scipydev/lib/python3.8/site-packages/_pytest/config/__init__.py", line 165 in main File "/home/bharath/scipy/scipy/build/testenv/lib/python3.8/site-packages/scipy/_lib/_testutils.py", line 69 in __call__ File "runtests.py", line 334 in main File "runtests.py", line 612 in <module> Segmentation fault (core dumped)
What might be causing this?
OS: Ubuntu 20.04.3 LTS
Python: 3.8
Numpy: 1.22.2 _______________________________________________ SciPy-Dev mailing list -- scipy-dev@python.org To unsubscribe send an email to scipy-dev-leave@python.org https://mail.python.org/mailman3/lists/scipy-dev.python.org/ Member address: ralf.gommers@gmail.com
Thanks for the prompt response. Yes, I tried rebuilding and found a fatal error caused by cblas.h and opened build issue #15609 on GitHub.
Hi, I built scipy again from the scipy-dev env (through environment.yml and the build was successful). However, the the test again seg faults at test_matfuncs.py. Here's the gdb backtrace: #0 0x00007ffff4a65900 in dgemv_n_BARCELONA () from /home/bharath/anaconda3/envs/scipy-dev/lib/python3.10/site-packages/numpy/core/../../../../libcblas.so.3 #1 0x0000000000000190 in ?? () #2 0x000000000000002f in ?? () #3 0x0000000000000000 in ?? () Should I open another issue on GitHub with the build log and backtrace or am I missing something trivial?
On Fri, Feb 25, 2022 at 10:55 AM Bharath K K <bharathkk0603@gmail.com> wrote:
Hi, I built scipy again from the scipy-dev env (through environment.yml and the build was successful). However, the the test again seg faults at test_matfuncs.py. Here's the gdb backtrace:
#0 0x00007ffff4a65900 in dgemv_n_BARCELONA () from /home/bharath/anaconda3/envs/scipy-dev/lib/python3.10/site-packages/numpy/core/../../../../libcblas.so.3 #1 0x0000000000000190 in ?? () #2 0x000000000000002f in ?? () #3 0x0000000000000000 in ?? ()
Should I open another issue on GitHub with the build log and backtrace or am I missing something trivial?
Yes please! This shouldn't be happening and looks like an issue in a BLAS library or our bindings to it; we need more info to be able to dig in, and a GitHub issue is a better place than the mailing list. Please Cc me (@rgommers) when you open the issue. Cheers, Ralf
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Ralf Gommers