Reopen the issue: sporco_cuda/tests/test_cbpdn.py *** stack smashing detected ***: python terminated #7
Comments
|
My environment is; ubuntu 16.04 Thank you. |
|
Could you try running the example scripts and report back on which ones work and which don't? |
|
I tried out your updated setup.py for #8 to the first machine showing on this #7 but still see the error with the same "stack smashing detected" in python setup.py test: (root) sekigh@04f0dd606f61:~/Windowsfolder/sporco-cuda$ python setup.py test sporco_cuda/tests/test_cbpdn.py *** stack smashing detected ***: python terminated Thread 0x00007f358a2d4700 (most recent call first): Current thread 0x00007f359d225700 (most recent call first): end of text |
|
The error log makes me suspect that this might actually be a problem in |
|
I just read your response on #8. Could you please also summarize the differences between the environment in which |
|
Hi, As for the result to python examples/big_cbpdn.py on the machine #7, unfortunately I have "stack smash error" again as follows: (root) sekigh@04f0dd606f61: The differences between installation on two machines include: Machine 1 configuration for #7 issue: ubuntu 16.04 sporco installation by source build/test/install Machine 2 configuration for #8 issue: ubuntu 18.04 sporco installation by conda install end of text |
|
Just to confirm, Could you try using python 3.8 via conda (see the script |
|
That is right！ Machine 2 works but machine 1 does not. My understanding is tools/install_conda.sh tries to install python3.8 based miniconda to the environment. Currently, I use pyenv/virtualenv. So I moved to sporco/tools directory and type: ./install_conda.sh /home/sekigh/.pyenv/versions where the new python 3.8 based environment successfully looks installed under /home/sekigh/.pyenv/versions. I see 3 new miniconda environments by pyenv versions; miniconda3 however, these three are all based on python 3.7.7 instead of 3.8. Is it OK ? python 3.8 may not be available for ubuntu16.04, because ubuntu 16.04 may be too old. Under miniconda3/envs/py38cu, I build/test/install sporco and sporco-cuda with source codes. Build works fine but test did not, showing *** stack smashing detected *** again. Full messages follow: (miniconda3/envs/py38cu) (base) sekigh@04f0dd606f61:~/Windowsfolder/sporco-cuda$ python setup.py test sporco_cuda/tests/test_cbpdn.py *** stack smashing detected ***: python terminated Thread 0x00007f6ce74c0700 (most recent call first): Current thread 0x00007f6cfa411700 (most recent call first): Moreover, python setup.py install is executed and try to run big_cbpdn.py again but failed again. (miniconda3/envs/py38cu) (base) sekigh@04f0dd606f61: end of text |
|
Strange that you end up with Python 3.7 instead of 3.8; I suppose it's related to your use of a virtualenv. I don't think it matters, though, since 3.7 is not very old. The Since the |
|
I double-checked python version used in py38cu and found it is 3.8.10 instead of 3.7.7. Therefore, it is reasonable. I delete previous sparco local repo and clone sporco rep again and run build/install from sporco source in environment py38cu. The results are not good; There two test results, one is cmp_cbpdn.py, and the other is big_cbpdn.py. The result of python ./examples/cmp_cbpdn.py shows cpu solver works fine but gpu solver fails. That is the opposite to your hypothesis. The result of python ./examples/big_cbpdn.py fails also. So gpu solver apparently fails. Find attached two execution logs below: (miniconda3/envs/py38cu) (base) sekigh@04f0dd606f61:~/Windowsfolder/sporco-cuda$ python ./examples/cmp_cbpdn.py
|
|
I have motivation to make sporco and sporco-cuda work properly on machine 1. That machine has two gpus for higher computation power compared with machine2, which has only one gpu. After solving #7 properly, I must consider how to combine gpu-based sporco capability with existing scripts based on tensorflow-gpu or pytorch-gpu to solve my problem efficiently. |
|
I found the way to work around *** stack smashing detected *** problem by changing installation method with trial and error. The workaround is the exact same way as one done for machine2, illustrating as;
Another weird phenomenon is when launching tests in the above 3) by eclipse debugger, you need to include as python library path /home/sekigh/.pyenv/versions/miniconda3/envs/py38cu/lib/python3.8/site-packages/sporco_cuda-0.0.6b1-py3.8-linux-x86_64.egg. Please make the installation procedure more robust and announce robust installation method on github pages. |
|
Thanks for your debugging efforts. I will certainly update the installation instructions if we can figure out which of the different steps you took made a critical difference. For example, is step 1. critical to getting it to work? How did you install sporco previously? From pypi, using pip? |
|
Now, "step 1 with conda install sporco" seems the most critical. The previous method replacing step 1 is; git clone https://github.com/bwohlberg/sporco.git After step 1, step 2 should be conducted. It seems that the step 2 with; git clone https://github.com/bwohlberg/sporco-cuda.git is successful without *** stack smashing detected *** errors, only after step 1 but not after the previous method replacing step 1. Interestingly, the major critical difference is that sporco_cuda-0.0.6b1-py3.8-linux-x86_64.egg is properly extracted to /home/sekigh/.pyenv/versions/miniconda3/envs/py38cu/lib/python3.8/site-packages in the former case but not in the second case. sporco_cuda-0.0.6b1-py3.8-linux-x86_64.egg has critical function to properly work. It is a critical clue for the reason why step1 and step2 works fine but the previous method not. The end of text |
|
So the only difference is whether you install sporco from the cloned repo (which leads to failure) or from conda (which leads to success)? I'm at a loss to explain this. |
|
Yes, that is right in short. My guess is that they are different somehow. |
|
What's really strange is that it's the installation method for sporco, and not sporco-cuda, that makes the difference. It's going to be difficult to add any guidance for the user to the documentation without understanding the underlying cause. |
|
My intuition to the cause to this problem is difference of sporco source scripts. I have no experience in making conda package from sources so I may be wrong. The source script produces sporco binary devian package version, sporco 0.2.0 py38h578d9bd_1 conda-forge, whereas, the source scripts shown on the sporco github produce different version, sporco 0.2.1. I observed these difference by conda list. Another point is that the former case lets sporco-cuda make sporco_cuda-0.0.6b1-py3.8-linux-x86_64.egg properly, whereas the latter case fails that egg. So *** stack smashing detected *** may happen. |
I have a problem similar to #3 (comment). Due to this I can not use cuda for sporco example script. How do I fix this ptoblem?
The error message is;
sporco_cuda/tests/test_cbpdn.py *** stack smashing detected ***: python terminated
Fatal Python error: Aborted
This happens when I ran
python setup.py test
during a process to build/test/install sporco-cuda by following installation instruction described in sporco-cuda 0.0.6b1 documentation,
git clone https://github.com/bwohlberg/sporco-cuda.git
cd sporco-cuda
export CUDAHOME=/usr/local/cuda-9.2
python setup.py build
python setup.py test
python setup.py install
Before running the above, I properly installed sporco and set up a symlink to sporco directory from the root directory of sporco-cuda.
See full error message attached below:
(anaconda3-2019.03) (base) sekigh@04f0dd606f61:~/Windowsfolder/sporco-cuda$ python setup.py test
running pytest
running egg_info
writing sporco_cuda.egg-info/PKG-INFO
writing dependency_links to sporco_cuda.egg-info/dependency_links.txt
writing requirements to sporco_cuda.egg-info/requires.txt
writing top-level names to sporco_cuda.egg-info/top_level.txt
reading manifest file 'sporco_cuda.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
no previously-included directories found matching 'docs/build'
writing manifest file 'sporco_cuda.egg-info/SOURCES.txt'
running build_ext
skipping 'sporco_cuda/util.c' Cython extension (up-to-date)
skipping 'sporco_cuda/cbpdn.c' Cython extension (up-to-date)
====================================== test session starts ======================================
platform linux -- Python 3.7.7, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /home/sekigh/Windowsfolder/sporco-cuda, configfile: pytest.ini, testpaths: sporco_cuda
collected 18 items
sporco_cuda/tests/test_cbpdn.py *** stack smashing detected ***: python terminated
Fatal Python error: Aborted
Thread 0x00007f3bc6d8e700 (most recent call first):
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pyfftw/interfaces/cache.py", line 224 in _run
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/threading.py", line 870 in run
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/threading.py", line 926 in _bootstrap_inner
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/threading.py", line 890 in _bootstrap
Current thread 0x00007f3bd9c5f700 (most recent call first):
File "/home/sekigh/Windowsfolder/sporco-cuda/sporco_cuda/tests/test_cbpdn.py", line 30 in test_01
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/python.py", line 183 in pytest_pyfunc_call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 87 in
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/python.py", line 1641 in runtest
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 162 in pytest_runtest_call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 87 in
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 255 in
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 311 in from_call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 255 in call_runtest_hook
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 215 in call_and_report
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 126 in runtestprotocol
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/runner.py", line 109 in pytest_runtest_protocol
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 87 in
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/main.py", line 348 in pytest_runtestloop
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 87 in
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/main.py", line 323 in _main
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/main.py", line 269 in wrap_session
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/main.py", line 316 in pytest_cmdline_main
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 87 in
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in call
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/_pytest/config/init.py", line 163 in main
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/ptr.py", line 220 in run_tests
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/ptr.py", line 209 in run
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/distutils/dist.py", line 985 in run_command
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/distutils/dist.py", line 966 in run_commands
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/distutils/core.py", line 148 in setup
File "/home/sekigh/.pyenv/versions/anaconda3-2019.03/lib/python3.7/site-packages/setuptools/init.py", line 153 in setup
File "setup.py", line 290 in
Aborted (core dumped)
(anaconda3-2019.03) (base) sekigh@04f0dd606f61:~/Windowsfolder/sporco-cuda$
The end of sentences
The text was updated successfully, but these errors were encountered: