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Published 20 hours ago • verified publisher icon zrqiao

Error in Installing the package

Open Anupam-5 opened this issue 8 months ago • 10 comments

  • 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

  • By downloading and using the cuDNN conda packages, you accept the terms and conditions of the NVIDIA cuDNN EULA - https://docs.nvidia.com/deeplearning/cudnn/sla/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

Anupam-5 avatar Jun 04 '24 10:06 Anupam-5