Running python run_alphafold_test. py encountered ImportError: /lib64/libc.so.6: version `GLIBC_2.28' not found

[Kangfengyuuuu]

Hello everyone, I have been using online tutorials to install AlphaFold 3 using Conda, and then running python run_alphafold_test.py. I encountered the problem：

ImportError: /lib64/libc.so.6: version `GLIBC_2.28' not found (required by /home/kangfengyu/miniconda3/envs/alphafold3/lib/python3.11/site-packages/rdkit/../rdkit.libs/libboost_filesystem-47d2d140.so.1.85.0)

After checking many tutorials, I was afraid that the Linux would crash. Now I don't know how to solve it. Has anyone encountered the same problem?

[Augustin-Zidek]

This looks like a problem with your Conda setup (rather than anything AlphaFold-specific), take a look at rdkit/rdkit#4756.

[vivek-rd]

I faced a similar issue (GLIBC_2.xx version not found) in a different project. If you installed the dependencies in an existing conda environment, try installing the dependencies in a new conda environment. This helped me resolve it.

[Kangfengyuuuu]

I faced a similar issue (GLIBC_2.xx version not found) in a different project. If you installed the dependencies in an existing conda environment, try installing the dependencies in a new conda environment. This helped me resolve it.

I now know that the program called libc.so.6 in Linux, which is incorrect. It should have called the dynamic library in conda, but I couldn't find libc.so.6 in my conda environment, and I downloaded GCC in a new conda environment, but I couldn't find libc.so.6 either. May I ask how you specifically solved it? There are many solutions online about libstd c++. so. 6, but I haven't found any specific way to solve libc. so. 6.

[Kangfengyuuuu]

This looks like a problem with your Conda setup (rather than anything AlphaFold-specific), take a look at rdkit/rdkit#4756.

I couldn't find a solution to libc. so. 6, so I tried installing Rdkit=2024.3.2 and ran run_alphafold_test. py without any more errors.
Does installing Rdkit=2024.3.2 have a significant impact on the prediction results of Alphafold 3?

[vivek-rd]

I faced a similar issue (GLIBC_2.xx version not found) in a different project. If you installed the dependencies in an existing conda environment, try installing the dependencies in a new conda environment. This helped me resolve it.

I now know that the program called libc.so.6 in Linux, which is incorrect. It should have called the dynamic library in conda, but I couldn't find libc.so.6 in my conda environment, and I downloaded GCC in a new conda environment, but I couldn't find libc.so.6 either. May I ask how you specifically solved it? There are many solutions online about libstd c++. so. 6, but I haven't found any specific way to solve libc. so. 6.

In my case, I started with a completely new conda environment. I did not install libc directly in the new environment and I just installed all the required dependencies and it resolved this issue.

[Kangfengyuuuu]

I faced a similar issue (GLIBC_2.xx version not found) in a different project. If you installed the dependencies in an existing conda environment, try installing the dependencies in a new conda environment. This helped me resolve it.

I now know that the program called libc.so.6 in Linux, which is incorrect. It should have called the dynamic library in conda, but I couldn't find libc.so.6 in my conda environment, and I downloaded GCC in a new conda environment, but I couldn't find libc.so.6 either. May I ask how you specifically solved it? There are many solutions online about libstd c++. so. 6, but I haven't found any specific way to solve libc. so. 6.

In my case, I started with a completely new conda environment. I did not install libc directly in the new environment and I just installed all the required dependencies and it resolved this issue.

Thank you for your answer! I solved the error of GLIBC-2.28 'not found' by reducing the version of rdkit. I will try reinstalling all dependencies in the new conda environment again.

[JeffersonPark1304]

@Kangfengyuuuu I faced the same issue. The following step solved my issue. Hopefully, it will help you

conda install libgcc