GLIBCXX error when attempting to import

[leeping]

Hi there,

The CI tests for geomeTRIC have failed with an ImportError recently, and the logs show a GLIBCXX version error when attempting to load OpenMM 8.0's shared library file:

E       ImportError: /usr/share/miniconda/lib/python3.9/site-packages/scipy/sparse/../../../../libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/share/miniconda/lib/python3.9/site-packages/openmm/../../../libOpenMM.so.8.0)

The log: https://github.com/leeping/geomeTRIC/actions/runs/4093539343/jobs/7059044624#step:5:1542

The env.yaml file used to set up the test environment: https://github.com/leeping/geomeTRIC/blob/master/devtools/conda-envs/latest.yaml

I'm not sure how this error could be reproduced because it's running on the CI server. Does it have to do with the Conda release being built on an OS that is newer than the testing OS?

Thanks,

• Lee-Ping

[leeping]

(That would be odd if it were the case because the OS is configured as ubuntu-latest).

[peastman]

I haven't encountered that error before, but it looks like a lot of people have run into it in various other packages. Do any of the solutions in https://stackoverflow.com/questions/72540359/glibcxx-3-4-30-not-found-for-librosa-in-conda-virtual-environment-after-tryin work?

[BenoitLF]

Did you manage to fix it ? I got the same error @leeping

[leeping]

@peastman , the top solution solved the issue; if I add gcc>=12.1.0 to the environment file, the error no longer occurs. However, Conda now takes about 30 minutes longer to solve the environment whereas it used to take ~10 minutes.

[peastman]

Use mamba instead of conda. It's much faster!

[leeping]

I probably should. :)

[biofe]

I ran into the same problem and solved it by extending the $LD_LIBRARY_PATH as suggested on stackoverflow. First I tried export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib but this didn't work. After some more inspection I inserted the conda path as first element: export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH which solved the issue for me. This looks to me like at some point openmm naturally doesn't consult the libraries from the conda environment, and further, only the first one in $LD_LIBRARY_PATH. So I suggest to change this to $CONDA_PREFIX/lib or at least to try all paths in $LD_LIBRARY_PATH since this issue took me a lot of time to resolve. Here are some lines of the error message in case this helps where to change this:

File "/home2020/home/institute/user/.conda/envs/my_env/lib/python3.11/site-packages/openmm/__init__.py", line 24, in <module>
from openmm.openmm import *
File "/home2020/home/institute/user/.conda/envs/my_env/lib/python3.11/site-packages/openmm/openmm.py", line 10, in <module>
from . import _openmm
ImportError: /usr/local/gcc/gcc-10.2.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home2020/home/institute/user/.conda/envs/my_env/lib/python3.11/site-packages/openmm/../../../libOpenMM.so.8.0)

[muziqaz]

I am running into this issue too, when checking python -m openmm.testInstallation. libstdc++.so.6 is already present on my system and has been cached by linker. conda install -c conda-forge libstdcxx-ng seem to have fixed the issue

[yar-nikolaev]

Solved by installing libstdcxx-ng via conda
conda install -c conda-forge libstdcxx-ng

The above command seem to have updated libstdc++.so.6 to include GLIBCXX_3.4.30 too.
Checking contents of libstdc++.so.6 before and after the update:
strings /home/ubuntu/anaconda3/envs/py38/lib/libstdc++.so.6 | grep GLIBCXX_3
Before:
GLIBCXX_3.4.1
...
GLIBCXX_3.4.28

After:
GLIBCXX_3.4.1
...
GLIBCXX_3.4.30

This was on Ubuntu 20.04. Initial error:
ImportError: /home/ubuntu/anaconda3/envs/py38/bin/../lib/libstdc++.so.6: version GLIBCXX_3.4.30 not found (required by /home/ubuntu/anaconda3/envs/py38/lib/python3.8/site-packages/openmm/../../../libOpenMM.so.8.0)

The default system-level libstdc++.so.6 also did not have the GLIBCXX_3.4.30:
strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
And it wasn't updating via apt-get - saying its already the oldest:
sudo apt-get install --only-upgrade libstdc++6
.. libstdc++6 is already the newest version (10.3.0-1ubuntu1~20.04).

[peastman]

Should we be including it as a dependency for the openmm conda package? Or is this a conda-forge bug and they should already be installing the right version?

[aloshbau]

I saw this error and conda install -c conda-forge libstdcxx-ng did NOT work for me, but export LD_LIBRARY_PATH=/home/.conda/envs/immune-builder/lib DID work.

ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/.conda/envs/immune-builder/lib/python3.11/site-packages/openmm/../../../libOpenMM.so.8.0)

conda install -c conda-forge libstdcxx-ng --> # All requested packages already installed.

strings ~/.conda/envs/immune-builder/lib/libstdc++.so.6 | grep 'GLIBCXX_3'
GLIBCXX_3.4
...
GLIBCXX_3.4.31

[mainguyenanhvu]

I guess we can remove all version of openMM and then re-install. This solution may work in case of other tools.
In this case, export LD_LIBRARY_PATH= help me. Thank @aloshbau .