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ketatam / DiffDock-PP

Implementation of DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models in PyTorch (ICLR 2023 - MLDD Workshop)
https://arxiv.org/abs/2304.03889
174 stars 35 forks source link

Installation Issue #19

Closed ELMIAR-0642 closed 8 months ago

ELMIAR-0642 commented 8 months ago

I get the following error while running the first two commands in -- Local, VM, Docker -- Kindly resolve the issue, I have checked the https://data.pyg.org/whl/torch-1.13.0+cu116.html also.

Command: pip install --no-cache-dir torch-scatter==2.0.9 torch-sparse==0.6.15 torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.13.0+cu116.html && pip install numpy dill tqdm pyyaml pandas biopandas scikit-learn biopython e3nn wandb tensorboard tensorboardX matplotlib

pip install --no-cache-dir  torch-scatter==2.0.9 torch-sparse==0.6.15 torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.13.0+cu116.html && pip install numpy dill tqdm pyyaml pandas biopandas scikit-learn biopython e3nn wandb tensorboard tensorboardX matplotlib
Looking in indexes: https://pypi.org/simple, https://packagecloud.io/github/git-lfs/pypi/simple
Looking in links: https://data.pyg.org/whl/torch-1.13.0+cu116.html
Collecting torch-scatter==2.0.9
  Downloading https://data.pyg.org/whl/torch-1.13.0%2Bcu116/torch_scatter-2.0.9-cp310-cp310-linux_x86_64.whl (9.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 9.4/9.4 MB 16.8 MB/s eta 0:00:00
Collecting torch-sparse==0.6.15
  Downloading https://data.pyg.org/whl/torch-1.13.0%2Bcu116/torch_sparse-0.6.15%2Bpt113cu116-cp310-cp310-linux_x86_64.whl (4.6 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.6/4.6 MB 9.4 MB/s eta 0:00:00
Collecting torch-cluster
  Downloading torch_cluster-1.6.3.tar.gz (54 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 54.5/54.5 kB 60.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting torch-spline-conv
  Downloading https://data.pyg.org/whl/torch-1.13.0%2Bcu116/torch_spline_conv-1.2.2%2Bpt113cu116-cp310-cp310-linux_x86_64.whl (868 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 868.3/868.3 kB 2.9 MB/s eta 0:00:00
Collecting torch-geometric
  Downloading torch_geometric-2.4.0-py3-none-any.whl.metadata (63 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.9/63.9 kB 62.4 MB/s eta 0:00:00
Collecting scipy (from torch-sparse==0.6.15)
  Downloading scipy-1.11.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.4/60.4 kB 182.3 MB/s eta 0:00:00
Collecting tqdm (from torch-geometric)
  Downloading tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.6/57.6 kB 183.5 MB/s eta 0:00:00
Collecting numpy (from torch-geometric)
  Downloading numpy-1.26.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.2/61.2 kB 157.0 MB/s eta 0:00:00
Collecting jinja2 (from torch-geometric)
  Downloading Jinja2-3.1.2-py3-none-any.whl (133 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.1/133.1 kB 199.0 MB/s eta 0:00:00
Collecting requests (from torch-geometric)
  Downloading requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting pyparsing (from torch-geometric)
  Downloading pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
Collecting scikit-learn (from torch-geometric)
  Downloading scikit_learn-1.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting psutil>=5.8.0 (from torch-geometric)
  Downloading psutil-5.9.6-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting MarkupSafe>=2.0 (from jinja2->torch-geometric)
  Downloading MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting charset-normalizer<4,>=2 (from requests->torch-geometric)
  Downloading charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests->torch-geometric)
  Downloading idna-3.4-py3-none-any.whl (61 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.5/61.5 kB 143.5 MB/s eta 0:00:00
Collecting urllib3<3,>=1.21.1 (from requests->torch-geometric)
  Downloading urllib3-2.0.7-py3-none-any.whl.metadata (6.6 kB)
Collecting certifi>=2017.4.17 (from requests->torch-geometric)
  Downloading certifi-2023.7.22-py3-none-any.whl.metadata (2.2 kB)
Collecting joblib>=1.1.1 (from scikit-learn->torch-geometric)
  Downloading joblib-1.3.2-py3-none-any.whl.metadata (5.4 kB)
Collecting threadpoolctl>=2.0.0 (from scikit-learn->torch-geometric)
  Downloading threadpoolctl-3.2.0-py3-none-any.whl.metadata (10.0 kB)
Downloading torch_geometric-2.4.0-py3-none-any.whl (1.0 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.0/1.0 MB 189.2 MB/s eta 0:00:00
Downloading psutil-5.9.6-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (283 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 283.6/283.6 kB 183.3 MB/s eta 0:00:00
Downloading numpy-1.26.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 18.2/18.2 MB 149.2 MB/s eta 0:00:00
Downloading pyparsing-3.1.1-py3-none-any.whl (103 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.1/103.1 kB 202.3 MB/s eta 0:00:00
Downloading requests-2.31.0-py3-none-any.whl (62 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.6/62.6 kB 115.7 MB/s eta 0:00:00
Downloading scikit_learn-1.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.8 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.8/10.8 MB 143.8 MB/s eta 0:00:00
Downloading scipy-1.11.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (36.4 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 36.4/36.4 MB 181.0 MB/s eta 0:00:00
Downloading tqdm-4.66.1-py3-none-any.whl (78 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.3/78.3 kB 126.9 MB/s eta 0:00:00
Downloading certifi-2023.7.22-py3-none-any.whl (158 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 158.3/158.3 kB 200.8 MB/s eta 0:00:00
Downloading charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 142.1/142.1 kB 169.0 MB/s eta 0:00:00
Downloading joblib-1.3.2-py3-none-any.whl (302 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 302.2/302.2 kB 124.7 MB/s eta 0:00:00
Downloading MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Downloading threadpoolctl-3.2.0-py3-none-any.whl (15 kB)
Downloading urllib3-2.0.7-py3-none-any.whl (124 kB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 124.2/124.2 kB 189.8 MB/s eta 0:00:00
Building wheels for collected packages: torch-cluster
  Building wheel for torch-cluster (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [45 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/torch_cluster
      copying torch_cluster/knn.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/typing.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/sampler.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/__init__.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/nearest.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/testing.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/rw.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/grid.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/radius.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/graclus.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      copying torch_cluster/fps.py -> build/lib.linux-x86_64-cpython-310/torch_cluster
      running egg_info
      writing torch_cluster.egg-info/PKG-INFO
      writing dependency_links to torch_cluster.egg-info/dependency_links.txt
      writing requirements to torch_cluster.egg-info/requires.txt
      writing top-level names to torch_cluster.egg-info/top_level.txt
      reading manifest file 'torch_cluster.egg-info/SOURCES.txt'
      reading manifest template 'MANIFEST.in'
      warning: no previously-included files matching '*' found under directory 'test'
      adding license file 'LICENSE'
      writing manifest file 'torch_cluster.egg-info/SOURCES.txt'
      running build_ext
      building 'torch_cluster._graclus_cpu' extension
      creating build/temp.linux-x86_64-cpython-310
      creating build/temp.linux-x86_64-cpython-310/csrc
      creating build/temp.linux-x86_64-cpython-310/csrc/cpu
      gcc -pthread -B /home/ubuntu/anaconda3/envs/diffdock_pp/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/ubuntu/anaconda3/envs/diffdock_pp/include -fPIC -O2 -isystem /home/ubuntu/anaconda3/envs/diffdock_pp/include -fPIC -DWITH_PYTHON -Icsrc -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/TH -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/THC -I/home/ubuntu/anaconda3/envs/diffdock_pp/include/python3.10 -c csrc/cpu/graclus_cpu.cpp -o build/temp.linux-x86_64-cpython-310/csrc/cpu/graclus_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_graclus_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
      gcc -pthread -B /home/ubuntu/anaconda3/envs/diffdock_pp/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/ubuntu/anaconda3/envs/diffdock_pp/include -fPIC -O2 -isystem /home/ubuntu/anaconda3/envs/diffdock_pp/include -fPIC -DWITH_PYTHON -Icsrc -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/TH -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/THC -I/home/ubuntu/anaconda3/envs/diffdock_pp/include/python3.10 -c csrc/graclus.cpp -o build/temp.linux-x86_64-cpython-310/csrc/graclus.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_graclus_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
      g++ -pthread -B /home/ubuntu/anaconda3/envs/diffdock_pp/compiler_compat -shared -Wl,-rpath,/home/ubuntu/anaconda3/envs/diffdock_pp/lib -Wl,-rpath-link,/home/ubuntu/anaconda3/envs/diffdock_pp/lib -L/home/ubuntu/anaconda3/envs/diffdock_pp/lib -Wl,-rpath,/home/ubuntu/anaconda3/envs/diffdock_pp/lib -Wl,-rpath-link,/home/ubuntu/anaconda3/envs/diffdock_pp/lib -L/home/ubuntu/anaconda3/envs/diffdock_pp/lib build/temp.linux-x86_64-cpython-310/csrc/cpu/graclus_cpu.o build/temp.linux-x86_64-cpython-310/csrc/graclus.o -L/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/lib -lc10 -ltorch -ltorch_cpu -ltorch_python -o build/lib.linux-x86_64-cpython-310/torch_cluster/_graclus_cpu.so -s
      building 'torch_cluster._graclus_cuda' extension
      creating build/temp.linux-x86_64-cpython-310/csrc/cuda
      gcc -pthread -B /home/ubuntu/anaconda3/envs/diffdock_pp/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/ubuntu/anaconda3/envs/diffdock_pp/include -fPIC -O2 -isystem /home/ubuntu/anaconda3/envs/diffdock_pp/include -fPIC -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/TH -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/THC -I/home/ubuntu/anaconda3/envs/diffdock_pp/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/include/python3.10 -c csrc/cpu/graclus_cpu.cpp -o build/temp.linux-x86_64-cpython-310/csrc/cpu/graclus_cpu.o -O2 -Wno-sign-compare -DAT_PARALLEL_OPENMP -fopenmp -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_graclus_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++14
      /home/ubuntu/anaconda3/envs/diffdock_pp/bin/nvcc -DWITH_PYTHON -DWITH_CUDA -Icsrc -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/torch/csrc/api/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/TH -I/home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/THC -I/home/ubuntu/anaconda3/envs/diffdock_pp/include -I/home/ubuntu/anaconda3/envs/diffdock_pp/include/python3.10 -c csrc/cuda/graclus_cuda.cu -o build/temp.linux-x86_64-cpython-310/csrc/cuda/graclus_cuda.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_BFLOAT16_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --expt-relaxed-constexpr --compiler-options '-fPIC' -O2 --expt-relaxed-constexpr -DTORCH_API_INCLUDE_EXTENSION_H -DPYBIND11_COMPILER_TYPE=\"_gcc\" -DPYBIND11_STDLIB=\"_libstdcpp\" -DPYBIND11_BUILD_ABI=\"_cxxabi1011\" -DTORCH_EXTENSION_NAME=_graclus_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -gencode=arch=compute_52,code=compute_52 -gencode=arch=compute_52,code=sm_52 -std=c++14
      In file included from csrc/cuda/graclus_cuda.cu:3:
      /home/ubuntu/anaconda3/envs/diffdock_pp/lib/python3.10/site-packages/torch/include/ATen/cuda/CUDAContext.h:10:10: fatal error: cusolverDn.h: No such file or directory
         10 | #include <cusolverDn.h>
            |          ^~~~~~~~~~~~~~
      compilation terminated.
      error: command '/home/ubuntu/anaconda3/envs/diffdock_pp/bin/nvcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for torch-cluster
  Running setup.py clean for torch-cluster
Failed to build torch-cluster
ERROR: Could not build wheels for torch-cluster, which is required to install pyproject.toml-based projects
ELMIAR-0642 commented 8 months ago

Solved by mentioning the version of torch-cluster. Updated command here:

pip install --no-cache-dir torch-scatter==2.0.9 torch-sparse==0.6.15 torch-cluster==1.6.0 torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.13.0+cu116.html && pip install numpy dill tqdm pyyaml pandas biopandas scikit-learn biopython e3nn wandb tensorboard tensorboardX matplotlib

Thanks to https://github.com/pyg-team/pytorch_geometric/issues/4460