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Error in Installing the package #47

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Anupam-5 opened this issue Jun 4, 2024 · 10 comments
Open

Error in Installing the package #47

Anupam-5 opened this issue Jun 4, 2024 · 10 comments

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@Anupam-5
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Anupam-5 commented Jun 4, 2024

  • PIGT version:
  • Python version : 3.10.12
  • Operating System : linux

Description

I am installing the package using commands in the tutorial but got stuck while using make environment.
I have changed the make file where the creating the conda environment command, I have just replaced the --force argument with the --yes argument as --force was deprecated, and then when I ran the make Environment command I got the following error

commands passed : git clone https://github.com/zrqiao/NeuralPLexer.git
cd NeuralPLexer/
make environment
make install

output:

conda env create -f environment_dev.yaml --yes
Channels:

  • nvidia
  • pytorch
  • pytorch3d
  • pyg
  • bioconda
  • conda-forge
  • salilab
  • 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/kinshuk/anaconda3/envs/neuralplexer_dev/bin/python', '-m', 'pip', 'install', '-U', '-r', '/home/kinshuk/Desktop/Anupam/NeuralPLexer/condaenv.2z4xf534.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting DLLogger@ git+https://github.com/NVIDIA/dllogger.git@0540a43971f4a8a16693a9de9de73c1072020769 (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 5))
Cloning https://github.com/NVIDIA/dllogger.git (to revision 0540a43971f4a8a16693a9de9de73c1072020769) to /tmp/pip-install-zog7c0p5/dllogger_10bd098947a7461ba2251987772bb861
Resolved https://github.com/NVIDIA/dllogger.git to commit 0540a43971f4a8a16693a9de9de73c1072020769
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@103d0370ad9ce07579c20fa9c889a632f9b16618 (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 6))
Cloning https://github.com/aqlaboratory/openfold.git (to revision 103d0370ad9ce07579c20fa9c889a632f9b16618) to /tmp/pip-install-zog7c0p5/openfold_608d1ba829ff41fe96a07c2107ff450c
Resolved https://github.com/aqlaboratory/openfold.git to commit 103d0370ad9ce07579c20fa9c889a632f9b16618
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting power-spherical@ git+https://****@github.com/zrqiao/power_spherical.git@290b1630c5f84e3bb0d61711046edcf6e47200d4 (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 7))
Using cached power_spherical-0.1.0-py3-none-any.whl
Collecting fair-esm@ git+https://github.com/facebookresearch/esm@57da016e5d740a9ac5bcf62c3689a42e88584bc (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 8))
Cloning https://github.com/facebookresearch/esm (to revision 57da016e5d740a9ac5bcf62c3689a42e88584bc) to /tmp/pip-install-zog7c0p5/fair-esm_a8fa202659b046c58d3af794d5d4f214
Resolved https://github.com/facebookresearch/esm to commit 57da016e5d740a9ac5bcf62c3689a42e88584bc
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting pytorch-lightning<2.0.0 (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1))
Using cached pytorch_lightning-1.9.5-py3-none-any.whl.metadata (23 kB)
Requirement already satisfied: torch-scatter in /home/kinshuk/.local/lib/python3.10/site-packages (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 2)) (2.1.2+pt20cu117)
Collecting fairscale (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 3))
Using cached fairscale-0.4.13-py3-none-any.whl
Collecting mendeleev (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4))
Using cached mendeleev-0.16.2-py3-none-any.whl.metadata (19 kB)
Requirement already satisfied: seaborn in /home/kinshuk/.local/lib/python3.10/site-packages (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (0.12.2)
Collecting seaborn (from -r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9))
Using cached seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB)
Requirement already satisfied: numpy>=1.17.2 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (1.24.3)
Requirement already satisfied: torch>=1.10.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (1.13.1)
Requirement already satisfied: tqdm>=4.57.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (4.64.1)
Requirement already satisfied: PyYAML>=5.4 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (6.0.1)
Requirement already satisfied: fsspec>2021.06.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (2023.9.0)
Requirement already satisfied: torchmetrics>=0.7.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (1.1.2)
Requirement already satisfied: packaging>=17.1 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (23.0)
Requirement already satisfied: typing-extensions>=4.0.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (4.9.0)
Requirement already satisfied: lightning-utilities>=0.6.0.post0 in /home/kinshuk/.local/lib/python3.10/site-packages (from pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (0.9.0)
Requirement already satisfied: Pygments<3.0.0,>=2.11.2 in /home/kinshuk/.local/lib/python3.10/site-packages (from mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4)) (2.14.0)
Requirement already satisfied: SQLAlchemy>=1.4.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4)) (2.0.24)
Requirement already satisfied: colorama<0.5.0,>=0.4.6 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4)) (0.4.6)
Requirement already satisfied: pandas>=1.0.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4)) (1.5.3)
Collecting pyfiglet<0.9,>=0.8.post1 (from mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4))
Using cached pyfiglet-0.8.post1-py2.py3-none-any.whl.metadata (1.3 kB)
Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in /home/kinshuk/.local/lib/python3.10/site-packages (from seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (3.7.0)
Requirement already satisfied: requests in /home/kinshuk/.local/lib/python3.10/site-packages (from fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (2.31.0)
Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /home/kinshuk/.local/lib/python3.10/site-packages (from fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (3.8.5)
Requirement already satisfied: contourpy>=1.0.1 in /home/kinshuk/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (1.0.7)
Requirement already satisfied: cycler>=0.10 in /home/kinshuk/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (4.38.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/kinshuk/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (1.4.4)
Requirement already satisfied: pillow>=6.2.0 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (10.3.0)
Requirement already satisfied: pyparsing>=2.3.1 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (3.1.2)
Requirement already satisfied: python-dateutil>=2.7 in /home/kinshuk/.local/lib/python3.10/site-packages (from matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from pandas>=1.0.0->mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4)) (2024.1)
Requirement already satisfied: greenlet!=0.4.17 in /home/kinshuk/.local/lib/python3.10/site-packages (from SQLAlchemy>=1.4.0->mendeleev->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 4)) (3.0.3)
Requirement already satisfied: nvidia-cuda-runtime-cu11==11.7.99 in /home/kinshuk/.local/lib/python3.10/site-packages (from torch>=1.10.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (11.7.99)
Requirement already satisfied: nvidia-cudnn-cu11==8.5.0.96 in /home/kinshuk/.local/lib/python3.10/site-packages (from torch>=1.10.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (8.5.0.96)
Requirement already satisfied: nvidia-cublas-cu11==11.10.3.66 in /home/kinshuk/.local/lib/python3.10/site-packages (from torch>=1.10.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (11.10.3.66)
Requirement already satisfied: nvidia-cuda-nvrtc-cu11==11.7.99 in /home/kinshuk/.local/lib/python3.10/site-packages (from torch>=1.10.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (11.7.99)
Requirement already satisfied: setuptools in /home/kinshuk/.local/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.10.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (63.4.3)
Requirement already satisfied: wheel in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.10.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (0.43.0)
Requirement already satisfied: attrs>=17.3.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (23.1.0)
Requirement already satisfied: charset-normalizer<4.0,>=2.0 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (3.3.2)
Requirement already satisfied: multidict<7.0,>=4.5 in /home/kinshuk/.local/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (6.0.4)
Requirement already satisfied: async-timeout<5.0,>=4.0.0a3 in /home/kinshuk/.local/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (4.0.3)
Requirement already satisfied: yarl<2.0,>=1.0 in /home/kinshuk/.local/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (1.9.2)
Requirement already satisfied: frozenlist>=1.1.1 in /home/kinshuk/.local/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (1.4.0)
Requirement already satisfied: aiosignal>=1.1.2 in /home/kinshuk/.local/lib/python3.10/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (1.3.1)
Requirement already satisfied: six>=1.5 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib!=3.6.1,>=3.4->seaborn->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 9)) (1.16.0)
Requirement already satisfied: idna<4,>=2.5 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from requests->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (3.7)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from requests->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (2.2.1)
Requirement already satisfied: certifi>=2017.4.17 in /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages (from requests->fsspec[http]>2021.06.0->pytorch-lightning<2.0.0->-r /home/kinshuk/Desktop/Anupam/NeuralPLexer/requirements.txt (line 1)) (2024.2.2)
Using cached pytorch_lightning-1.9.5-py3-none-any.whl (829 kB)
Using cached mendeleev-0.16.2-py3-none-any.whl (353 kB)
Using cached seaborn-0.13.2-py3-none-any.whl (294 kB)
Using cached pyfiglet-0.8.post1-py2.py3-none-any.whl (865 kB)
Building wheels for collected packages: openfold, fair-esm
Building wheel for openfold (setup.py): started
Building wheel for openfold (setup.py): finished with status 'error'
Running setup.py clean for openfold
Building wheel for fair-esm (pyproject.toml): started
Building wheel for fair-esm (pyproject.toml): finished with status 'done'
Created wheel for fair-esm: filename=fair_esm-2.0.1-py3-none-any.whl size=95476 sha256=fdb2c54969377d9547c9a5d7e43f3a7f735e2c851e5a532c9dc3f663446d5642
Stored in directory: /tmp/pip-ephem-wheel-cache-pn0e_5jr/wheels/c3/14/10/35edcfc6a0e8958b1a19ca6669a28a7972b72691f2f717fb08
Successfully built fair-esm
Failed to build openfold

Pip subprocess error:
Running command git clone --filter=blob:none --quiet https://github.com/NVIDIA/dllogger.git /tmp/pip-install-zog7c0p5/dllogger_10bd098947a7461ba2251987772bb861
Running command git rev-parse -q --verify 'sha^0540a43971f4a8a16693a9de9de73c1072020769'
Running command git fetch -q https://github.com/NVIDIA/dllogger.git 0540a43971f4a8a16693a9de9de73c1072020769
Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-zog7c0p5/openfold_608d1ba829ff41fe96a07c2107ff450c
Running command git rev-parse -q --verify 'sha^103d0370ad9ce07579c20fa9c889a632f9b16618'
Running command git fetch -q https://github.com/aqlaboratory/openfold.git 103d0370ad9ce07579c20fa9c889a632f9b16618
Running command git checkout -q 103d0370ad9ce07579c20fa9c889a632f9b16618
Running command git clone --filter=blob:none --quiet https://github.com/facebookresearch/esm /tmp/pip-install-zog7c0p5/fair-esm_a8fa202659b046c58d3af794d5d4f214
WARNING: Did not find branch or tag '57da016e5d740a9ac5bcf62c3689a42e88584bc', assuming revision or ref.
Running command git checkout -q 57da016e5d740a9ac5bcf62c3689a42e88584bc
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [168 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/openfold
copying openfold/config.py -> build/lib.linux-x86_64-cpython-310/openfold
copying openfold/init.py -> build/lib.linux-x86_64-cpython-310/openfold
creating build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/msa.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/triangular_multiplicative_update.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/template.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/dropout.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/evoformer.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/structure_module.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/pair_transition.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/primitives.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/outer_product_mean.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/heads.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/init.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/embedders.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/model.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/triangular_attention.py -> build/lib.linux-x86_64-cpython-310/openfold/model
copying openfold/model/torchscript.py -> build/lib.linux-x86_64-cpython-310/openfold/model
creating build/lib.linux-x86_64-cpython-310/openfold/resources
copying openfold/resources/init.py -> build/lib.linux-x86_64-cpython-310/openfold/resources
creating build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/templates.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/data_transforms.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/feature_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/mmcif_parsing.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/init.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/input_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/parsers.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/data_pipeline.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/data_modules.py -> build/lib.linux-x86_64-cpython-310/openfold/data
copying openfold/data/errors.py -> build/lib.linux-x86_64-cpython-310/openfold/data
creating build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/exponential_moving_average.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/lr_schedulers.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/trace_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/superimposition.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/tensor_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/loss.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/import_weights.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/script_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/suppress_output.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/validation_metrics.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/init.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/feats.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/precision_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/callbacks.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/checkpointing.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/seed.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/rigid_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/logger.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/argparse.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
copying openfold/utils/chunk_utils.py -> build/lib.linux-x86_64-cpython-310/openfold/utils
creating build/lib.linux-x86_64-cpython-310/openfold/np
copying openfold/np/residue_constants.py -> build/lib.linux-x86_64-cpython-310/openfold/np
copying openfold/np/init.py -> build/lib.linux-x86_64-cpython-310/openfold/np
copying openfold/np/protein.py -> build/lib.linux-x86_64-cpython-310/openfold/np
creating build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/utils.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/init.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/kalign.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/hhsearch.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/jackhmmer.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
copying openfold/data/tools/hhblits.py -> build/lib.linux-x86_64-cpython-310/openfold/data/tools
creating build/lib.linux-x86_64-cpython-310/openfold/utils/kernel
copying openfold/utils/kernel/attention_core.py -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel
copying openfold/utils/kernel/init.py -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel
creating build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/amber_minimize.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/utils.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/init.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/relax.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
copying openfold/np/relax/cleanup.py -> build/lib.linux-x86_64-cpython-310/openfold/np/relax
running egg_info
creating openfold.egg-info
writing openfold.egg-info/PKG-INFO
writing dependency_links to openfold.egg-info/dependency_links.txt
writing top-level names to openfold.egg-info/top_level.txt
writing manifest file 'openfold.egg-info/SOURCES.txt'
reading manifest file 'openfold.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'openfold.egg-info/SOURCES.txt'
/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/command/build_py.py:153: SetuptoolsDeprecationWarning: Installing 'openfold.utils.kernel.csrc' as data is deprecated, please list it in packages.
!!

      ############################
      # Package would be ignored #
      ############################
      Python recognizes 'openfold.utils.kernel.csrc' as an importable package,
      but it is not listed in the `packages` configuration of setuptools.
  
      'openfold.utils.kernel.csrc' has been automatically added to the distribution only
      because it may contain data files, but this behavior is likely to change
      in future versions of setuptools (and therefore is considered deprecated).
  
      Please make sure that 'openfold.utils.kernel.csrc' is included as a package by using
      the `packages` configuration field or the proper discovery methods
      (for example by using `find_namespace_packages(...)`/`find_namespace:`
      instead of `find_packages(...)`/`find:`).
  
      You can read more about "package discovery" and "data files" on setuptools
      documentation page.
  
  
  !!
  
    check.warn(importable)
  creating build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda_stub.cpp -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/compat.h -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda_kernel.cu -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  copying openfold/utils/kernel/csrc/softmax_cuda.cpp -> build/lib.linux-x86_64-cpython-310/openfold/utils/kernel/csrc
  running build_ext
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/tmp/pip-install-zog7c0p5/openfold_608d1ba829ff41fe96a07c2107ff450c/setup.py", line 112, in <module>
      setup(
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/__init__.py", line 87, in setup
      return distutils.core.setup(**attrs)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
      return run_commands(dist)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
      dist.run_commands()
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_commands
      self.run_command(cmd)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
      cmd_obj.run()
    File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 368, in run
      self.run_command("build")
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
      self.distribution.run_command(command)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
      cmd_obj.run()
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/command/build.py", line 24, in run
      super().run()
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 132, in run
      self.run_command(cmd_name)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
      self.distribution.run_command(command)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/dist.py", line 1217, in run_command
      super().run_command(command)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 992, in run_command
      cmd_obj.run()
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 79, in run
      _build_ext.run(self)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
      _build_ext.build_ext.run(self)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 346, in run
      self.build_extensions()
    File "/home/kinshuk/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 499, in build_extensions
      _check_cuda_version(compiler_name, compiler_version)
    File "/home/kinshuk/.local/lib/python3.10/site-packages/torch/utils/cpp_extension.py", line 386, in _check_cuda_version
      raise RuntimeError(CUDA_MISMATCH_MESSAGE.format(cuda_str_version, torch.version.cuda))
  RuntimeError:
  The detected CUDA version (12.3) mismatches the version that was used to compile
  PyTorch (11.7). Please make sure to use the same CUDA versions.
  
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for openfold
ERROR: Could not build wheels for openfold, which is required to install pyproject.toml-based projects

failed

CondaEnvException: Pip failed

make: *** [Makefile:87: environment] Error 1
@ejmeitz
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ejmeitz commented Jun 4, 2024 •
edited
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I had similar issues, anaconda isn't smart enough for some reason to install everything with the same version of CUDA.

Edit: The env should be python 3.9 to work with openfold

I installed with these commands to get it to work on my end:

  • conda install pytorch==2.0.1 torchvision==0.15.2 pytorch-cuda=11.7 -c pytorch -c nvidia
  • conda install -c fvcore -c iopath -c conda-forge fvcore iopath
  • conda install pytorch3d -c pytorch3d

Removed pytorch-scatter from the requirements.txt
Without this here it will not install a CUDA version

  • conda install pytorch-scatter -c pyg

  • conda install setuptools=69.5.1 biopython prody deprecated hydra-core=1.1.1 dm-tree ml-collections networkx pypdb pytest dataclasses msgpack-python msgpack-numpy numpy openbabel pandas rdkit rmsd tmalign tensorboard jupyter tqdm python-lmdb vim wandb -c pyg -c bioconda -c conda-forge

Needed for openfold to install correctly or else it will pull the system CUDA and will throw err if mismatched

  • conda install cudatoolkit-dev=11.7

Remove torch-scatter from requirements.txt or you'll get wrong version

  • pip install -r requirements.txt

  • make install

@Anupam-5
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Author

Anupam-5 commented Jun 5, 2024

I had similar issues, anaconda isn't smart enough for some reason to install everything with the same version of CUDA.

I installed with these commands to get it to work on my end:

  • conda install pytorch==2.0.1 torchvision==0.15.2 pytorch-cuda=11.7 -c pytorch -c nvidia
  • conda install -c fvcore -c iopath -c conda-forge fvcore iopath
  • conda install pytorch3d -c pytorch3d

Removed pytorch-scatter from the requirements.txt Without this here it will not install a CUDA version

  • conda install pytorch-scatter -c pyg
  • conda install setuptools=69.5.1 biopython prody deprecated hydra-core=1.1.1 dm-tree ml-collections networkx pypdb pytest dataclasses msgpack-python msgpack-numpy numpy openbabel pandas rdkit rmsd tmalign tensorboard jupyter tqdm python-lmdb vim wandb -c pyg -c bioconda -c conda-forge

Needed for openfold to install correctly or else it will pull the system CUDA and will throw err if mismatched

  • conda install cudatoolkit-dev=11.7

Remove torch-scatter from requirements.txt or you'll get wrong version

  • pip install -r requirements.txt
  • make install

Thanks for replying. I am using cuda version 12.3, should I downgrade my cuda version to 11.7 or it will work for it too.

@ejmeitz
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ejmeitz commented Jun 5, 2024

It might work, you can try just changing all the CUDA versions from 11.7 to 12.3. You might have to change other versions though see:
https://pytorch.org/get-started/previous-versions/
https://github.com/facebookresearch/pytorch3d/releases/tag/v0.7.6

Also my driver version is 12.3, the CUDA you install to anaconda just needs to be older than your driver as far as I understand.

@Anupam-5
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Anupam-5 commented Jun 7, 2024

hey @ejmeitz !!
Thanks for your help.
I tried as you suggested to do the installation was successful but when I ran the inference command I got the following error :

(neuralplexer_dev) kinshuk@kinshuk-lab:~/Desktop/Anupam/NeuralPLexer$ neuralplexer-inference --task=batched_structure_sampling
--input-receptor ./protein.pdb
--input-ligand ./ligand.sdf
--use-template --input-template 4djh.pdb
--out-path ./output
--model-checkpoint ./neuralplexermodels_downstream_datasets_predictions/models/complex_structure_prediction.ckpt
--n-samples 16
--chunk-size 4
--num-steps=40
--cuda
--sampler=langevin_simulated_annealing
/home/kinshuk/.local/lib/python3.10/site-packages/torchvision/io/image.py:13: UserWarning: Failed to load image Python extension: '/home/kinshuk/.local/lib/python3.10/site-packages/torchvision/image.so: undefined symbol: _ZN3c104cuda20CUDACachingAllocator9allocatorE'If you don't plan on using image functionality from torchvision.io, you can ignore this warning. Otherwise, there might be something wrong with your environment. Did you have libjpeg or libpng installed before building torchvision from source?
warn(
Traceback (most recent call last):
File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/bin/neuralplexer-inference", line 33, in
sys.exit(load_entry_point('neuralplexer', 'console_scripts', 'neuralplexer-inference')())
File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/bin/neuralplexer-inference", line 25, in importlib_load_entry_point
return next(matches).load()
File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/importlib/metadata/init.py", line 171, in load
module = import_module(match.group('module'))
File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/importlib/init.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1050, in _gcd_import
File "", line 1027, in _find_and_load
File "", line 1006, in _find_and_load_unlocked
File "", line 688, in _load_unlocked
File "", line 883, in exec_module
File "", line 241, in _call_with_frames_removed
File "/home/kinshuk/Desktop/Anupam/NeuralPLexer/neuralplexer/inference.py", line 27, in
from neuralplexer.model.wrappers import NeuralPlexer
File "/home/kinshuk/Desktop/Anupam/NeuralPLexer/neuralplexer/model/wrappers.py", line 8, in
from pytorch3d.ops import corresponding_points_alignment
File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages/pytorch3d/ops/init.py", line 7, in
from .ball_query import ball_query
File "/home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages/pytorch3d/ops/ball_query.py", line 10, in
from pytorch3d import _C
ImportError: /home/kinshuk/anaconda3/envs/neuralplexer_dev/lib/python3.10/site-packages/pytorch3d/_C.cpython-310-x86_64-linux-gnu.so: undefined symbol: _ZNK3c107SymBool10guard_boolEPKcl

Can anyone suggest what to do.

@ejmeitz
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ejmeitz commented Jun 7, 2024

Yea I got this the first few times.... I'd look at conda list | grep torch and conda list | grep cuda and make sure they all have the same version of CUDA and that nothing that should be installed with CUDA is installed as CPU.

That last line with pytorch3d I always got, so I'm guessing it somehow installed a CPU version for something.

@mavericb
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I had similar issues, anaconda isn't smart enough for some reason to install everything with the same version of CUDA.

I installed with these commands to get it to work on my end:

  • conda install pytorch==2.0.1 torchvision==0.15.2 pytorch-cuda=11.7 -c pytorch -c nvidia
  • conda install -c fvcore -c iopath -c conda-forge fvcore iopath
  • conda install pytorch3d -c pytorch3d

Removed pytorch-scatter from the requirements.txt Without this here it will not install a CUDA version

  • conda install pytorch-scatter -c pyg
  • conda install setuptools=69.5.1 biopython prody deprecated hydra-core=1.1.1 dm-tree ml-collections networkx pypdb pytest dataclasses msgpack-python msgpack-numpy numpy openbabel pandas rdkit rmsd tmalign tensorboard jupyter tqdm python-lmdb vim wandb -c pyg -c bioconda -c conda-forge

Needed for openfold to install correctly or else it will pull the system CUDA and will throw err if mismatched

  • conda install cudatoolkit-dev=11.7

Remove torch-scatter from requirements.txt or you'll get wrong version

  • pip install -r requirements.txt
  • make install

thanks!!! this worked for me :)

@yipy0005
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yipy0005 commented Aug 2, 2024

Hi @ejmeitz, I tried your method and it all works well till it is trying to install openfold and gave the following error:

Collecting openfold@ git+https://github.com/aqlaboratory/openfold.git@103d0370ad9ce07579c20fa9c889a632f9b16618 (from -r openfold.txt (line 1))
  Cloning https://github.com/aqlaboratory/openfold.git (to revision 103d0370ad9ce07579c20fa9c889a632f9b16618) to /tmp/pip-install-wcnn9gow/openfold_d31e60aaff8a4ffbbe81d298275ae557
  Running command git clone --filter=blob:none --quiet https://github.com/aqlaboratory/openfold.git /tmp/pip-install-wcnn9gow/openfold_d31e60aaff8a4ffbbe81d298275ae557
  Running command git rev-parse -q --verify 'sha^103d0370ad9ce07579c20fa9c889a632f9b16618'
  Running command git fetch -q https://github.com/aqlaboratory/openfold.git 103d0370ad9ce07579c20fa9c889a632f9b16618
  Running command git checkout -q 103d0370ad9ce07579c20fa9c889a632f9b16618
  Resolved https://github.com/aqlaboratory/openfold.git to commit 103d0370ad9ce07579c20fa9c889a632f9b16618
  Preparing metadata (setup.py) ... error
  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 "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-install-wcnn9gow/openfold_d31e60aaff8a4ffbbe81d298275ae557/setup.py", line 19, in <module>
          import torch
        File "/home/yipy/miniforge3/envs/neuralplexer_dev/lib/python3.10/site-packages/torch/__init__.py", line 229, in <module>
          from torch._C import *  # noqa: F403
      ImportError: /home/yipy/miniforge3/envs/neuralplexer_dev/lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent
      [end of output]

  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.

Any ideas on how I can resolve the problem? 😄

Best regards,
Yew Mun

@ejmeitz
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ejmeitz commented Aug 2, 2024

Not exactly sure, its a little weird that the error is in the cpu part of torch. If you do conda list | grep torch and conda list | grep cuda be sure that torch actually installed a GPU version and that it matches the version of cuda that got installed. Beyond that I'm not really sure.

@yipy0005
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yipy0005 commented Aug 2, 2024 

mamba list | grep torch
pytorch                   2.0.1           py3.10_cuda11.7_cudnn8.5.0_0    pytorch
pytorch-cuda              11.7                 h778d358_5    pytorch
pytorch-lightning         1.9.5                    pypi_0    pypi
pytorch-mutex             1.0                        cuda    pytorch
pytorch-scatter           2.1.2           py310_torch_2.0.0_cu117    pyg
pytorch3d                 0.7.7           py310_cu117_pyt201    pytorch3d
torchmetrics              1.4.0.post0              pypi_0    pypi
torchtriton               2.0.0                     py310    pytorch
torchvision               0.15.2              py310_cu117    pytorch

mamba list | grep cuda
cuda-cudart               11.7.99                       0    nvidia
cuda-cupti                11.7.101                      0    nvidia
cuda-libraries            11.7.1                        0    nvidia
cuda-nvrtc                11.7.99                       0    nvidia
cuda-nvtx                 11.7.91                       0    nvidia
cuda-runtime              11.7.1                        0    nvidia
cuda-version              12.6                          3    nvidia
cudatoolkit-dev           11.7.0               h1de0b5d_6    conda-forge
pytorch                   2.0.1           py3.10_cuda11.7_cudnn8.5.0_0    pytorch
pytorch-cuda              11.7                 h778d358_5    pytorch
pytorch-mutex             1.0                        cuda    pytorch

I would say that torch has installed a GPU version (?)

@ejmeitz
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ejmeitz commented Aug 2, 2024

I think you need python 3.9 actually. OpenFold has that as a requirement and my env is also 3.9 but you have 3.10. Hopefully that works.

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@yipy0005 @ejmeitz @mavericb @Anupam-5