Segmentation fault (core dumped) #50
Comments
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Hi @Kerro-junior. Unfortunately I can't reproduce this problem. Can you pleas try to run
It is known that
How did you install the libraries manually? With PS: I took the freedom to re-format your issue. Please use code blocks and inline code blocks to make things a bit more readable than plain text. |
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For your questions, I manually installed the libraries by the consequence you provided in yml file with conda.(but libmolgrid with pip). I try use I will look into the incompatibilities between libmolgrid and openbabel later, and tried use mamba to create environment. |
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sorry to bother you, but I still cannot use mamba to install the gnina-torch, actually I do not know why I can't install mamba in conda, it always do you have any idea of the reason of |
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Unfortunately I can't reproduce the problem on my end, therefore it is a bit difficult to know what's going on.
Since nothing is printed before the segmentation fault (not even the initial
As mentioned above, conda is notoriously slow in these situations. In my experience, this was happening when you try to install new things in an already bloated environment (an environment with many different packages, or the
If you look at the |
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Thanks for your advice, I have successfully installed mambaforge into my base environment, and I have successfully used mamba to create gninatorch environment( I notive this env uses python3.11), then use BUT, the pytest still has troubles: Then I check some basic information about python: then I tried base environment to do pytest, still error |
There is clearly something off with your configuration, since it is picking up Python not from the environment.
As mentioned previously, this is not recommended by the |
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Thanks, I have re-active the Sorry to bother you, but I have no idea how to handle this libmolgrid import error... |
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Can you please try to build an environment with Python 3.10 and see if something changes? |
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I firstly use So I delete the specific gcc I defined in the ~/.bashrc, and run the pytest again: HOW STRANGE it is! the python of gninatorch turn into python3.11 again?I tried again 'mamba update python=3.10' to update python into 3.10 but failed.SO I remove the env and modify the Then I So finally after I installed the gninatorch with mamba, BUT it constantly report errors: |
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I learned that it's the problem of my gcc, FYI my gcc is assigned by adding I would be grateful if you can teach how to solve the problem |
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@Kerro-junior thanks for checking. Since this is a problem with how your setup is (mis-)configured, I can't help much. You will have to fix how things are setup on your end. What I can suggest is to try to install a newer version of GCC from |
Test Error
System Details
CentOS7 Linux server
Anaconda environment (python3.9)
I have created this environment and install all the libraries manually.
(It takes hours in the 'solving' process when running
conda env create -f devtools/conda-envs/gninatorch.yaml, so I quit and created a environment 'gninatorch' and install libraries one by one as the yml shows)After all dependencies have been installed (I additionally installed
scikit-learn-intelexas thescikit-learnsuggests), I runpython -m pip install .thegninatorch 0.0.2+3.ge46cb51successfully installed. BUT It could not success at$ pytest --cov==gninatorch.The text was updated successfully, but these errors were encountered: