Installation error - GLIBC_2.34 related

[Huanle]

Hi @gcorso ,

Thanks heaps for bringing diffdock to the community.

I was struggling with the installation of this program.

It seemed to be ok until I started to run the example command.

command:

python -m inference --protein_ligand_csv data/protein_ligand_example_csv.csv --out_dir results/user_predictions_small --inference_steps 20 --samples_per_complex 40 --batch_size 10 --actual_steps 18 --no_final_step_noise

Error message: <Traceback (most recent call last): File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/huanle/sw/structual_bioinformatics/protein_nucleotides/DiffDock-main/inference.py", line 10, in from torch_geometric.loader import DataLoader File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch_geometric/init.py", line 4, in import torch_geometric.data File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch_geometric/data/init.py", line 1, in from .data import Data File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch_geometric/data/data.py", line 9, in from torch_sparse import SparseTensor File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch_sparse/init.py", line 18, in torch.ops.load_library(spec.origin) File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch/_ops.py", line 220, in load_library ctypes.CDLL(path) File "/home/huanle/miniconda3/envs/diffdock/lib/python3.9/ctypes/init.py", line 374, in init self._handle = _dlopen(self._name, mode) OSError: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /home/popular/hl_miniconda3/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch_sparse/_version_cpu.so) (diffdock) huanle@node1:~/.../DiffDock-main$ vi /home/huanle/miniconda3/envs/diffdock/lib/python3.9/ctypes/init.py

The error message indicates that the GLBC_2.34 is missing though I think it is installed. Because this strings /home/popular/hl_miniconda3/miniconda3/envs/diffdock/lib/python3.9/site-packages/torch_sparse/_version_cpu.so | grep GLIB yields: <GLIBC_2.34 GLIBC_2.4 GLIBC_2.2.5 GLIBCXX_3.4.9 GLIBCXX_3.4>

Can you help me fix this problem? Thanks a lot!

[asarigun]

You can check my solution here!