Bedinka
commented
6 months ago Hi ! Having this issue too, unable to crete the env, even its getting created I am unable to run on it. `(base) dina@:~/Documents/PPI_WDLLM/openfold$ mamba env create -n openfold_env -f environment.yml 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/dina/miniconda3/envs/openfold_env/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/dina/Documents/PPI_WDLLM/openfold/condaenv.preb3c5c.requirements.txt', '--exists-action=b'] Pip subprocess output: Collecting git+https://github.com/NVIDIA/dllogger.git (from -r /home/dina/Documents/PPI_WDLLM/openfold/condaenv.preb3c5c.requirements.txt (line 3)) Cloning https://github.com/NVIDIA/dllogger.git to /tmp/pip-req-build-71c6bsk5 Resolved https://github.com/NVIDIA/dllogger.git to commit 0540a43971f4a8a16693a9de9de73c1072020769 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting git+https://github.com/Dao-AILab/flash-attention.git@5b838a8 (from -r /home/dina/Documents/PPI_WDLLM/openfold/condaenv.preb3c5c.requirements.txt (line 4)) Cloning https://github.com/Dao-AILab/flash-attention.git (to revision 5b838a8) to /tmp/pip-req-build-ayvfskhx
Pip subprocess error: Running command git clone --filter=blob:none --quiet https://github.com/NVIDIA/dllogger.git /tmp/pip-req-build-71c6bsk5 Running command git clone --filter=blob:none --quiet https://github.com/Dao-AILab/flash-attention.git /tmp/pip-req-build-ayvfskhx WARNING: Did not find branch or tag '5b838a8', assuming revision or ref. Running command git checkout -q 5b838a8 fatal: unable to access 'https://github.com/Dao-AILab/flash-attention.git/': Failed to connect to github.com port 443 after 135026 ms: Couldn't connect to server fatal: could not fetch a8e8349e1ba482c43ec63bc4676fba32fe393f67 from promisor remote error: subprocess-exited-with-error
× git checkout -q 5b838a8 did not run successfully. │ exit code: 128 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× git checkout -q 5b838a8 did not run successfully. │ exit code: 128 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
failed
CondaEnvException: Pip failed
(base) dina@:~/Documents/PPI_WDLLM/openfold$ conda env create -n openfold_env -f environment.yml
CondaValueError: prefix already exists: /home/dina/miniconda3/envs/openfold_env
(base) dina@:~/Documents/PPI_WDLLM/openfold$ conda env create -n openfold_env2 -f environment.yml 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/dina/miniconda3/envs/openfold_env2/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/dina/Documents/PPI_WDLLM/openfold/condaenv.7a4lsks6.requirements.txt', '--exists-action=b'] Pip subprocess output: Collecting git+https://github.com/NVIDIA/dllogger.git (from -r /home/dina/Documents/PPI_WDLLM/openfold/condaenv.7a4lsks6.requirements.txt (line 3)) Cloning https://github.com/NVIDIA/dllogger.git to /tmp/pip-req-build-958chdta Resolved https://github.com/NVIDIA/dllogger.git to commit 0540a43971f4a8a16693a9de9de73c1072020769 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting git+https://github.com/Dao-AILab/flash-attention.git@5b838a8 (from -r /home/dina/Documents/PPI_WDLLM/openfold/condaenv.7a4lsks6.requirements.txt (line 4)) Cloning https://github.com/Dao-AILab/flash-attention.git (to revision 5b838a8) to /tmp/pip-req-build-xv8wg8u4 Resolved https://github.com/Dao-AILab/flash-attention.git to commit 5b838a8 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'error'
Pip subprocess error: Running command git clone --filter=blob:none --quiet https://github.com/NVIDIA/dllogger.git /tmp/pip-req-build-958chdta Running command git clone --filter=blob:none --quiet https://github.com/Dao-AILab/flash-attention.git /tmp/pip-req-build-xv8wg8u4 WARNING: Did not find branch or tag '5b838a8', assuming revision or ref. Running command git checkout -q 5b838a8 Running command git submodule update --init --recursive -q error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [8 lines of output]
Traceback (most recent call last):
File "
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
× Encountered error while generating package metadata. ╰─> See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details.
failed
CondaEnvException: Pip failed
(base) dina@:~/Documents/PPI_WDLLM/openfold$ conda env list
conda environments:
# base * /home/dina/miniconda3 esmfold /home/dina/miniconda3/envs/esmfold myenv /home/dina/miniconda3/envs/myenv openfold /home/dina/miniconda3/envs/openfold openfold_env /home/dina/miniconda3/envs/openfold_env openfold_env2 /home/dina/miniconda3/envs/openfold_env2
(base) dina@:~/Documents/PPI_WDLLM/openfold$ conda activate openfold_env (openfold_env) dina@:~/Documents/PPI_WDLLM/openfold$ scripts/install_third_party_dependencies.sh --2024-04-16 17:22:08-- https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt Resolving git.scicore.unibas.ch (git.scicore.unibas.ch)... 131.152.229.50 Connecting to git.scicore.unibas.ch (git.scicore.unibas.ch)|131.152.229.50|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 9119 (8,9K) [text/plain] Saving to: ‘openfold/resources/stereo_chemical_props.txt’
stereo_chemical_props.txt 100%[=================================================>] 8,91K --.-KB/s in 0s
Last-modified header missing -- time-stamps turned off. 2024-04-16 17:22:09 (50,3 MB/s) - ‘openfold/resources/stereo_chemical_props.txt’ saved [9119/9119]
ln: failed to create symbolic link 'tests/test_data/alphafold/common/stereo_chemical_props.txt': File exists
Traceback (most recent call last):
File "/home/dina/Documents/PPI_WDLLM/openfold/setup.py", line 19, in
luiswyss
shams-mehdi
sachinkadyan7
I clone the repo, cd into it, run the provided command
mamba env create -n openfold_env -f environment.ymland run into the following error: