I am getting error in the installation step. My system is Ubuntu 22.04.3 LTS and my Cuda version is 12.3. Could anyone please let me know what is the problem could be? Thank you very much!
conda env create --name=fastfold -f environment.yml
Retrieving notices: ...working... done
Channels:
- conda-forge
- bioconda
- pytorch
- defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: | By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html
done
Installing pip dependencies: / Ran pip subprocess with arguments:
['/home/henry/miniconda3/envs/fastfold/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting biopython==1.79 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 1))
Downloading biopython-1.79-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting dm-tree==0.1.6 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 2))
Downloading dm_tree-0.1.6-cp38-cp38-manylinux_2_24_x86_64.whl.metadata (1.7 kB)
Collecting ml-collections==0.1.0 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 3))
Downloading ml_collections-0.1.0-py3-none-any.whl.metadata (18 kB)
Collecting PyYAML==5.4.1 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 4))
Downloading PyYAML-5.4.1-cp38-cp38-manylinux1_x86_64.whl.metadata (2.1 kB)
Collecting requests==2.26.0 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 5))
Downloading requests-2.26.0-py2.py3-none-any.whl.metadata (4.8 kB)
Collecting scipy==1.7.1 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 6))
Downloading scipy-1.7.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (2.2 kB)
Collecting tqdm==4.62.2 (from -r /home/henry/soft/FastFold/condaenv.hrf191cn.requirements.txt (line 7))
Downloading tqdm-4.62.2-py2.py3-none-any.whl.metadata (56 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.0/57.0 kB 4.8 kB/s eta 0:00:00
Pip subprocess error:
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProtocolError('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))': /simple/biopython/
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out. (read timeout=15)")': /packages/0f/02/dac61d8f7e32fa803b6fa57a7daffb0d2993efde8503aca29082f1d1ce87/scipy-1.7.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata
ERROR: Ignored the following versions that require a different python version: 1.11.0 Requires-Python <3.13,>=3.9; 1.11.0rc1 Requires-Python <3.13,>=3.9; 1.11.0rc2 Requires-Python <3.13,>=3.9; 1.11.1 Requires-Python <3.13,>=3.9; 1.11.2 Requires-Python <3.13,>=3.9; 1.11.3 Requires-Python <3.13,>=3.9; 1.11.4 Requires-Python >=3.9; 1.12.0 Requires-Python >=3.9; 1.12.0rc1 Requires-Python >=3.9; 1.12.0rc2 Requires-Python >=3.9; 1.13.0rc1 Requires-Python >=3.9
ERROR: Could not find a version that satisfies the requirement typing-extensions==4.3.0 (from versions: none)
ERROR: No matching distribution found for typing-extensions==4.3.0
failed
CondaEnvException: Pip failed
Hi all,
I am getting error in the installation step. My system is Ubuntu 22.04.3 LTS and my Cuda version is 12.3. Could anyone please let me know what is the problem could be? Thank you very much!
Best, Henry