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labstreaminglayer / pylsl

Python bindings (pylsl) for liblsl
MIT License
142 stars 58 forks source link

crash with sklearn on my system #40

Closed xloem closed 3 years ago

xloem commented 3 years ago

This happens only when pylsl is imported first:

>>> import pylsl
>>> import sklearn
*** Error in `python3': free(): invalid pointer: 0x00007f6446a63bc0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81299)[0x7f645fb39299]
/lib64/libstdc++.so.6(_ZNSt6locale5_Impl16_M_install_facetEPKNS_2idEPKNS_5facetE+0x142)[0x7f64467cded2]
/lib64/libstdc++.so.6(_ZNSt6locale5_ImplC1Em+0x1e3)[0x7f64467ce323]
/lib64/libstdc++.so.6(+0x71295)[0x7f64467cf295]
/lib64/libpthread.so.0(+0x620b)[0x7f646059520b]
/lib64/libstdc++.so.6(+0x712e1)[0x7f64467cf2e1]
/lib64/libstdc++.so.6(_ZNSt6localeC2Ev+0x13)[0x7f64467cf323]
/lib64/libstdc++.so.6(_ZNSt8ios_base4InitC2Ev+0xbc)[0x7f64467cc17c]
/home/user/.local/lib/python3.8/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-38-x86_64-linux-gnu.so(+0x77f0)[0x7f64464ae7f0]
/lib64/ld-linux-x86-64.so.2(+0xf9c3)[0x7f64610499c3]
/lib64/ld-linux-x86-64.so.2(+0x1459e)[0x7f646104e59e]
/lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f64610497d4]
/lib64/ld-linux-x86-64.so.2(+0x13b8b)[0x7f646104db8b]
/lib64/libdl.so.2(+0xfab)[0x7f646038bfab]
/lib64/ld-linux-x86-64.so.2(+0xf7d4)[0x7f64610497d4]
/lib64/libdl.so.2(+0x15ad)[0x7f646038c5ad]
/lib64/libdl.so.2(dlopen+0x31)[0x7f646038c041]
/usr/local/lib/libpython3.8.so.1.0(_PyImport_FindSharedFuncptr+0x183)[0x7f6460c7d573]
/usr/local/lib/libpython3.8.so.1.0(_PyImport_LoadDynamicModuleWithSpec+0x2ae)[0x7f6460c344ae]
/usr/local/lib/libpython3.8.so.1.0(+0x24fb81)[0x7f6460c31b81]
/usr/local/lib/libpython3.8.so.1.0(+0x112e13)[0x7f6460af4e13]
/usr/local/lib/libpython3.8.so.1.0(PyVectorcall_Call+0x5d)[0x7f6460a961bd]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0xa630)[0x7f6460a59860]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x13ab)[0x7f6460c02c4b]
/usr/local/lib/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x15f)[0x7f6460a9386f]                                                                                                      [85/118]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0xa925)[0x7f6460a59b55]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x9023)[0x7f6460a58253]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x889a)[0x7f6460a57aca]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x889a)[0x7f6460a57aca]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x889a)[0x7f6460a57aca]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
/usr/local/lib/libpython3.8.so.1.0(+0xb22bc)[0x7f6460a942bc]
/usr/local/lib/libpython3.8.so.1.0(_PyObject_CallMethodIdObjArgs+0x10f)[0x7f6460a9452f]
/usr/local/lib/libpython3.8.so.1.0(PyImport_ImportModuleLevelObject+0x4ff)[0x7f6460c32f1f]
/usr/local/lib/libpython3.8.so.1.0(+0x21ad2f)[0x7f6460bfcd2f]
/usr/local/lib/libpython3.8.so.1.0(PyCFunction_Call+0x147)[0x7f6460a963b7]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0xa630)[0x7f6460a59860]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x13ab)[0x7f6460c02c4b]
/usr/local/lib/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x15f)[0x7f6460a9386f]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x889a)[0x7f6460a57aca]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x13ab)[0x7f6460c02c4b]
/usr/local/lib/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x15f)[0x7f6460a9386f]
/usr/local/lib/libpython3.8.so.1.0(+0xb22bc)[0x7f6460a942bc]
/usr/local/lib/libpython3.8.so.1.0(_PyObject_CallMethodIdObjArgs+0x10f)[0x7f6460a9452f]
/usr/local/lib/libpython3.8.so.1.0(PyImport_ImportModuleLevelObject+0x62c)[0x7f6460c3304c]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0xb500)[0x7f6460a5a730]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x13ab)[0x7f6460c02c4b]
/usr/local/lib/libpython3.8.so.1.0(PyEval_EvalCodeEx+0x93)[0x7f6460c033c3]
/usr/local/lib/libpython3.8.so.1.0(PyEval_EvalCode+0x3b)[0x7f6460c0340b]
/usr/local/lib/libpython3.8.so.1.0(+0x21bbb2)[0x7f6460bfdbb2]
/usr/local/lib/libpython3.8.so.1.0(+0x112e13)[0x7f6460af4e13]
/usr/local/lib/libpython3.8.so.1.0(PyVectorcall_Call+0x5d)[0x7f6460a961bd]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0xa630)[0x7f6460a59860]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x13ab)[0x7f6460c02c4b]                                                                                                   [52/118]
/usr/local/lib/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x15f)[0x7f6460a9386f]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0xa925)[0x7f6460a59b55]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
/usr/local/lib/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x9023)[0x7f6460a58253]
/usr/local/lib/libpython3.8.so.1.0(+0x6c0a1)[0x7f6460a4e0a1]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fd:02 402913258                          /usr/local/bin/python3.8
00600000-00601000 r--p 00000000 fd:02 402913258                          /usr/local/bin/python3.8
00601000-00602000 rw-p 00001000 fd:02 402913258                          /usr/local/bin/python3.8
012ad000-017f2000 rw-p 00000000 00:00 0                                  [heap]
7f6440000000-7f6440021000 rw-p 00000000 00:00 0 
7f6440021000-7f6444000000 ---p 00000000 00:00 0 
7f64464a7000-7f6446559000 r-xp 00000000 fd:02 432834388                  /home/user/.local/lib/python3.8/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-38-x86_64-linux-gnu.so
7f6446559000-7f6446758000 ---p 000b2000 fd:02 432834388                  /home/user/.local/lib/python3.8/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-38-x86_64-linux-gnu.so
7f6446758000-7f644675a000 rw-p 000b1000 fd:02 432834388                  /home/user/.local/lib/python3.8/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-38-x86_64-linux-gnu.so
7f644675a000-7f644675e000 rw-p 00000000 00:00 0 
7f644675e000-7f6446847000 r-xp 00000000 fd:02 76539                      /usr/lib64/libstdc++.so.6.0.19
7f6446847000-7f6446a46000 ---p 000e9000 fd:02 76539                      /usr/lib64/libstdc++.so.6.0.19
7f6446a46000-7f6446a4e000 r--p 000e8000 fd:02 76539                      /usr/lib64/libstdc++.so.6.0.19
7f6446a4e000-7f6446a50000 rw-p 000f0000 fd:02 76539                      /usr/lib64/libstdc++.so.6.0.19
7f6446a50000-7f6446a65000 rw-p 00000000 00:00 0 
7f6446aae000-7f6446ab7000 r-xp 00000000 fd:02 142071259                  /home/user/.local/lib/python3.8/site-packages/scipy/_lib/_uarray/_uarray.cpython-38-x86_64-linux-gnu.so
7f6446ab7000-7f6446cb7000 ---p 00009000 fd:02 142071259                  /home/user/.local/lib/python3.8/site-packages/scipy/_lib/_uarray/_uarray.cpython-38-x86_64-linux-gnu.so
7f6446cb7000-7f6446cb8000 rw-p 00009000 fd:02 142071259                  /home/user/.local/lib/python3.8/site-packages/scipy/_lib/_uarray/_uarray.cpython-38-x86_64-linux-gnu.so
7f6446cb8000-7f6446cf8000 rw-p 00000000 00:00 0 
7f6446cf8000-7f6446d06000 r-xp 00000000 fd:02 36621292                   /home/user/.local/lib/python3.8/site-packages/scipy/_lib/_ccallback_c.cpython-38-x86_64-linux-gnu.so
7f6446d06000-7f6446f06000 ---p 0000e000 fd:02 36621292                   /home/user/.local/lib/python3.8/site-packages/scipy/_lib/_ccallback_c.cpython-38-x86_64-linux-gnu.so
7f6446f06000-7f6446f08000 rw-p 0000e000 fd:02 36621292                   /home/user/.local/lib/python3.8/site-packages/scipy/_lib/_ccallback_c.cpython-38-x86_64-linux-gnu.so
7f6446f08000-7f6446fc8000 rw-p 00000000 00:00 0 
7f6446fc8000-7f6447064000 r-xp 00000000 fd:02 1190750                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_generator.cpython-38-x86_64-linux-gnu.so
7f6447064000-7f6447264000 ---p 0009c000 fd:02 1190750                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_generator.cpython-38-x86_64-linux-gnu.so
7f6447264000-7f6447288000 rw-p 0009c000 fd:02 1190750                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_generator.cpython-38-x86_64-linux-gnu.so
7f6447288000-7f644728b000 rw-p 00000000 00:00 0                                                                                                                                       [19/118]
7f644728b000-7f6447296000 r-xp 00000000 fd:02 1190744                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_sfc64.cpython-38-x86_64-linux-gnu.so
7f6447296000-7f6447496000 ---p 0000b000 fd:02 1190744                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_sfc64.cpython-38-x86_64-linux-gnu.so
7f6447496000-7f6447497000 rw-p 0000b000 fd:02 1190744                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_sfc64.cpython-38-x86_64-linux-gnu.so
7f6447497000-7f6447498000 rw-p 00000000 00:00 0 
7f6447498000-7f64474a7000 r-xp 00000000 fd:02 1190743                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_pcg64.cpython-38-x86_64-linux-gnu.so
7f64474a7000-7f64476a7000 ---p 0000f000 fd:02 1190743                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_pcg64.cpython-38-x86_64-linux-gnu.so
7f64476a7000-7f64476a9000 rw-p 0000f000 fd:02 1190743                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_pcg64.cpython-38-x86_64-linux-gnu.so
7f64476a9000-7f64476bb000 r-xp 00000000 fd:02 1190753                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_philox.cpython-38-x86_64-linux-gnu.so
7f64476bb000-7f64478ba000 ---p 00012000 fd:02 1190753                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_philox.cpython-38-x86_64-linux-gnu.so
7f64478ba000-7f64478bc000 rw-p 00011000 fd:02 1190753                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_philox.cpython-38-x86_64-linux-gnu.so
7f64478bc000-7f64478bd000 rw-p 00000000 00:00 0 
7f64478bd000-7f64478d5000 r-xp 00000000 fd:02 1190756                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_mt19937.cpython-38-x86_64-linux-gnu.so
7f64478d5000-7f6447ad4000 ---p 00018000 fd:02 1190756                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_mt19937.cpython-38-x86_64-linux-gnu.so
7f6447ad4000-7f6447ad7000 rw-p 00017000 fd:02 1190756                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_mt19937.cpython-38-x86_64-linux-gnu.so
7f6447ad7000-7f6447b30000 r-xp 00000000 fd:02 1190769                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_bounded_integers.cpython-38-x86_64-linux-gnu.so
7f6447b30000-7f6447d30000 ---p 00059000 fd:02 1190769                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_bounded_integers.cpython-38-x86_64-linux-gnu.so
7f6447d30000-7f6447d32000 rw-p 00059000 fd:02 1190769                    /home/user/.local/lib/python3.8/site-packages/numpy/random/_bounded_integers.cpython-38-x86_64-linux-gnu.so
7f6447d32000-7f6447d34000 rw-p 00000000 00:00 0 
7f6447d34000-7f6447d4b000 r-xp 00000000 fd:02 146419526                  /usr/local/lib/python3.8/lib-dynload/_sha3.cpython-38-x86_64-linux-gnu.so
7f6447d4b000-7f6447f4b000 ---p 00017000 fd:02 146419526                  /usr/local/lib/python3.8/lib-dynload/_sha3.cpython-38-x86_64-linux-gnu.so
7f6447f4b000-7f6447f4c000 r--p 00017000 fd:02 146419526                  /usr/local/lib/python3.8/lib-dynload/_sha3.cpython-38-x86_64-linux-gnu.so
7f6447f4c000-7f6447f4d000 rw-p 00018000 fd:02 146419526                  /usr/local/lib/python3.8/lib-dynload/_sha3.cpython-38-x86_64-linux-gnu.so
7f6447f4d000-7f6447f58000 r-xp 00000000 fd:02 147016158                  /usr/local/lib/python3.8/lib-dynload/_blake2.cpython-38-x86_64-linux-gnu.so
7f6447f58000-7f6448157000 ---p 0000b000 fd:02 147016158                  /usr/local/lib/python3.8/lib-dynload/_blake2.cpython-38-x86_64-linux-gnu.so
7f6448157000-7f6448158000 r--p 0000a000 fd:02 147016158                  /usr/local/lib/python3.8/lib-dynload/_blake2.cpython-38-x86_64-linux-gnu.so
7f6448158000-7f6448159000 rw-p 0000b000 fd:02 147016158                  /usr/local/lib/python3.8/lib-dynload/_blake2.cpython-38-x86_64-linux-gnu.so
7f6448159000-7f64481b9000 r-xp 00000000 fd:02 91067                      /usr/lib64/libpcre.so.1.2.0
7f64481b9000-7f64483b9000 ---p 00060000 fd:02 91067                      /usr/lib64/libpcre.so.1.2.0
7f64483b9000-7f64483ba000 r--p 00060000 fd:02 91067                      /usr/lib64/libpcre.so.1.2.0
7f64483ba000-7f64483bb000 rw-p 00061000 fd:02 91067                      /usr/lib64/libpcre.so.1.2.0
7f64483bb000-7f64483df000 r-xp 00000000 fd:02 91079                      /usr/lib64/libselinux.so.1
7f64483df000-7f64485de000 ---p 00024000 fd:02 91079                      /usr/lib64/libselinux.so.1
7f64485de000-7f64485df000 r--p 00023000 fd:02 91079                      /usr/lib64/libselinux.so.1
7f64485df000-7f64485e0000 rw-p 00024000 fd:02 91079                      /usr/lib64/libselinux.so.1
7f64485e0000-7f64485e2000 rw-p 00000000 00:00 0 
7f64485e2000-7f64485f8000 r-xp 00000000 fd:02 626528                     /usr/lib64/libresolv-2.17.so
7f64485f8000-7f64487f8000 ---p 00016000 fd:02 626528                     /usr/lib64/libresolv-2.17.so
7f64487f8000-7f64487f9000 r--p 00016000 fd:02 626528                     /usr/lib64/libresolv-2.17.so
7f64487f9000-7f64487fa000 rw-p 00017000 fd:02 626528                     /usr/lib64/libresolv-2.17.so
7f64487fa000-7f64487fc000 rw-p 00000000 00:00 0 
7f64487fc000-7f64487ff000 r-xp 00000000 fd:02 98056                      /usr/lib64/libkeyutils.so.1.5
7f64487ff000-7f64489fe000 ---p 00003000 fd:02 98056                      /usr/lib64/libkeyutils.so.1.5
7f64489fe000-7f64489ff000 r--p 00002000 fd:02 98056                      /usr/lib64/libkeyutils.so.1.5
7f64489ff000-7f6448a00000 rw-p 00003000 fd:02 98056                      /usr/lib64/libkeyutils.so.1.5
7f6448a00000-7f6448a0e000 r-xp 00000000 fd:02 91016                      /usr/lib64/libkrb5support.so.0.1
7f6448a0e000-7f6448c0e000 ---p 0000e000 fd:02 91016                      /usr/lib64/libkrb5support.so.0.1
7f6448c0e000-7f6448c0f000 r--p 0000e000 fd:02 91016                      /usr/lib64/libkrb5support.so.0.1
7f6448c0f000-7f6448c10000 rw-p 0000f000 fd:02 91016                      /usr/lib64/libkrb5support.so.0.1
7f6448c10000-7f6448c41000 r-xp 00000000 fd:02 91008                      /usr/lib64/libk5crypto.so.3.1
7f6448c41000-7f6448e40000 ---p 00031000 fd:02 91008                      /usr/lib64/libk5crypto.so.3.1Aborted (core dumped)
cboulay commented 3 years ago

I see you're using python 3.8 but I need more detailed information.

Exactly what version of Python 3? What version of scikit-learn and how was it installed? How did you install pylsl? What version do you have?

Not that it's worth much, but I just did a quick test with python 3.8.5, scikit-learn 0.23.2, and the latest pylsl from github, ON WINDOWS, and I didn't encounter any problems. I don't have time to test in Ubuntu right now; maybe tomorrow.

cboulay commented 3 years ago

I remembered I had a WSL2 Ubuntu 20.04 environment so I tested there quickly (this time pylsl from pypi) and also didn't have any problems.

(test_pylsl) chad@AAA:/mnt/c/Users/chad$ pip install pylsl
Collecting pylsl
  Downloading pylsl-1.14.0-py2.py3-none-manylinux2010_x86_64.whl (815 kB)
     |████████████████████████████████| 815 kB 3.2 MB/s
Installing collected packages: pylsl
Successfully installed pylsl-1.14.0

Python 3.8.5 (default, Sep  4 2020, 07:30:14)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.19.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import pylsl

In [2]: import sklearn

In [3]: exit()
xloem commented 3 years ago

I had set the packages up with pip3 install pylsl && pip3 install sklearn. I'm using a git checkout of python3.8.

$ python3 --version
Python 3.8.7+
cpython]$ git describe
v3.8.7-3-g285b38c3a8

It will take me some time to test any further. I tried to install pylsl from git and I'm having some troubles setting it up; the setup isn't working right now anymore.

xloem commented 3 years ago

Okay, it looks like I had some old liblsl.so laying around that was causing the issue. Upgrading liblsl.so resolved it. Thanks for your patience.

xloem commented 3 years ago

To clarify, the resolution to this issue is from installing pylsl from git, not from the binary liblsl. After installing from git once, the .whl file gets cached and is reinstalled when outside git.