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.

[njzjz]

It's still confusing to me - you showed you installed v2.9.2 but the meta.yaml file you provided is v2.8.1.
Do you have any log file or package file?

[Zhang-pchao]

I apologize for the confusion. I tested the plumed versions from v2.8.1 to v2.9.2, and I've attached the log file from the v2.9.2 update based on this meta.yaml. The log indicates that "Needed DSO lib/libstdc++.so.6 found in defaults/linux-64," but I am still encountering the same issue. Thank you!
log.txt

[njzjz]

INFO (plumed,lib/libstdc++.so.6.0.29): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package defaults/noarch::sysroot_linux-64==2.17=h57e8cba_10
INFO (plumed,lib/libstdc++.so.6.0.29): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package defaults/noarch::sysroot_linux-64==2.17=h57e8cba_10
INFO (plumed,lib/libstdc++.so.6.0.29): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/ld-linux-x86-64.so.2 found in CDT/compiler package defaults/noarch::sysroot_linux-64==2.17=h57e8cba_10
INFO (plumed,lib/libstdc++.so.6.0.29): Needed DSO lib/libgcc_s.so.1 found in defaults/linux-64::libgcc-ng==11.2.0=h1234567_1 (and also in this package)

Per the log, this package contains a libstdc++.so file (and other files that don't belong to plumed) that is conflict with the original one.

[Zhang-pchao]

Given the deprecation notice for the deepmd-kit-recipes repository, is there a new recipes link for updating PLUMED to be compatible with DeePMD-kit v3, similar to the previous PLUMED feedstock for DeePMD-kit v2? Thanks in advance!

[Zhang-pchao]

Attempting to mirror the workflow from the feedstock allows LibTorch-enabled PLUMED to be installed, but it breaks the bundled LAMMPS executable inside the Conda environment.

The steps here avoid that incompatibility by compiling each dependency from source in a controlled prefix.