Bioemu[md] Hpacker Error

[WillDeSnoo]

Hello,

I am attempting to use bioemu[md] to reconstruct side chains, but am encountering errors.

When I attempt to run the following command:
python -m bioemu.sidechain_relax --pdb-path ./topology.pdb --xtc-path ./samples.xtc

I get this error:
python: symbol lookup error: /home/desnoow/miniconda3/envs/bioemu_md/lib/python3.12/site-packages/OpenMM.libs/lib/plugins/libOpenMMCUDA.so: undefined symbol: _ZN6OpenMM8Platform21registerKernelFactoryERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS_13KernelFactoryE

Do you have any recommendations to fix this or alternative methods to reconstruct side chains?

Best,
Will

[nw13slx]

Hi Will, thanks for reporting. Could you please provide your cuda details. and also how do you manage your python environment?

[WillDeSnoo]

Hello, thank you for the swift response. Here are the cuda details:
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2024 NVIDIA Corporation
Built on Thu_Sep_12_02:18:05_PDT_2024
Cuda compilation tools, release 12.6, V12.6.77
Build cuda_12.6.r12.6/compiler.34841621_0

My python environment is a fresh conda environment with python 3.12, and I installed bioemu[md] with pip. So I created the environment with these commands:

conda create -n bioemu_md python==3.12
conda activate bioemu_md
pip install bioemu[md]

[nw13slx]

Could you please show your results of conda list openmm and pip list|grep Open

I think I need to fix the installation dependency on pip, which may take a while. For now, could you please try

pip uninstall openmm openmm-cuda-12
pip install "openmm-cuda-12==8.2.0" openmm==8.2.0

[WillDeSnoo]

Here are the outputs of the conda list openmm and pip list|grep Open, respectively:

Name Version Build Channel

openmm 8.2.0 pypi_0 pypi
openmm-cuda-12 8.4.0.post2 pypi_0 pypi

OpenMM 8.2.0
OpenMM-CUDA-12 8.4.0.post2

And your suggestion fixed my issue, thank you for your help!

[thempel]

Thanks @nw13slx . I think the older versions of openMM are broken on pypi (compare this issue openmm/openmm#5141). I'm going to upgrade requirements to 8.4.0.