GLIBCXX Version Error in DeepMD v3.0.0 after Updating PLUMED

[Zhang-pchao]

Hi Developers,

I successfully installed the DeepMD v3.0.0 environment via Conda, and it works fine for tasks like fine-tuning. However, I encountered an issue when attempting to update the PLUMED version by following the plumed-feedstock guide (adding custom CV C++ files) using conda build.

After updating PLUMED, I found that training a model or running MD in DeepMD v3.0.0 fails with the following error:

/path/deepmd-kit_v3/setup/envs/dpmdkit_v3.0.0_vcv/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /path/deepmd-kit_v3/setup/envs/dpmdkit_v3.0.0_vcv/bin/../lib/./././libicuuc.so.75)

This issue does not occur with DeepMD v2. I was able to update PLUMED in the same way without encountering any problems.

Request

Could you please provide guidance on how to resolve this issue for DeepMD v3.0.0? Any help would be greatly appreciated!

Thanks in advance!

[njzjz]

Please use conda list to check the version of libstdcxx-ng.

It seems you mix the packages from the conda-forge and anaconda channels, which is not recommended.

[Zhang-pchao]

Before Update:

libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-devel_linux-64  11.4.0             h8f596e0_113    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
plumed                    2.9.2           mpi_openmpi_h02da92d_0    conda-forge

After Update:

libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-devel_linux-64  11.4.0             h8f596e0_113    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
plumed                    2.9.2                h4ecb923_1    local

Observations

• The libstdcxx-ng package version (14.2.0) and build (h4852527_1) remain unchanged before and after the update.
• The plumed package source changed from conda-forge to local after the update.

Questions

Is it expected that libstdcxx-ng remains unchanged after the PLUMED update?

[njzjz]

Does your libstdc++.so contain GLIBCXX_3.4.30?

echo $CONDA_PREFIX
strings $CONDA_PREFIX/lib/libstdc++.so | grep GLIBCXX_3.4.30

Expected output:

GLIBCXX_3.4.30
GLIBCXX_3.4.30

[Zhang-pchao]

Before the update, the expected output matched what you provided, but after the update, there is no output. How can I fix this? Thank you for your response.