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How to install torch-scatter==1.3.1?

See original GitHub issue

I am trying to install 3D Part Assembly and they have the following requirements

https://github.com/AntheaLi/3DPartAssembly/blob/master/requirements.txt

numpy==1.16.0
opencv-python==4.2.0
pillow==6.2.0
pytorch==1.3.1
scikit-image==0.15.0
scikit-learn==0.21.3
scipy==1.3.1
setuptools==41.4.0
torchvision==0.4.2
torch-scatter==1.3.1
blender==2.7.9
bpy

When I am running the jupyter notebook

using pip install torch-scatter I am getting this

Collecting torch-scatter
  Using cached torch_scatter-2.0.5.tar.gz (20 kB)
Building wheels for collected packages: torch-scatter
  Building wheel for torch-scatter (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdta70kw/torch-scatter/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdta70kw/torch-scatter/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-15s2z_fx
       cwd: /tmp/pip-install-gdta70kw/torch-scatter/
  Complete output (47 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/torch_scatter
  copying torch_scatter/utils.py -> build/lib.linux-x86_64-3.8/torch_scatter
  copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.8/torch_scatter
  copying torch_scatter/scatter.py -> build/lib.linux-x86_64-3.8/torch_scatter
  copying torch_scatter/segment_csr.py -> build/lib.linux-x86_64-3.8/torch_scatter
  copying torch_scatter/placeholder.py -> build/lib.linux-x86_64-3.8/torch_scatter
  copying torch_scatter/segment_coo.py -> build/lib.linux-x86_64-3.8/torch_scatter
  creating build/lib.linux-x86_64-3.8/torch_scatter/composite
  copying torch_scatter/composite/logsumexp.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
  copying torch_scatter/composite/std.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
  copying torch_scatter/composite/__init__.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
  copying torch_scatter/composite/softmax.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
  running build_ext
  building 'torch_scatter._scatter' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/tmp
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc/cpu
  creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc/cuda
  x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITH_CUDA -I/tmp/pip-install-gdta70kw/torch-scatter/csrc -I/usr/lib/python3/dist-packages/torch/include -I/usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include -I/usr/lib/python3/dist-packages/torch/include/TH -I/usr/lib/python3/dist-packages/torch/include/THC -I/usr/include/python3.8 -c /tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.o -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_scatter -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++14
  In file included from /usr/lib/python3/dist-packages/torch/include/ATen/Parallel.h:149,
                   from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/utils.h:3,
                   from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/nn/cloneable.h:5,
                   from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/nn.h:3,
                   from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/all.h:7,
                   from /usr/lib/python3/dist-packages/torch/include/torch/extension.h:4,
                   from /tmp/pip-install-gdta70kw/torch-scatter/csrc/cpu/scatter_cpu.h:3,
                   from /tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.cpp:4:
  /usr/lib/python3/dist-packages/torch/include/ATen/ParallelOpenMP.h:84: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     84 | #pragma omp parallel for if ((end - begin) >= grain_size)
        |
  In file included from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/python.h:12,
                   from /usr/lib/python3/dist-packages/torch/include/torch/extension.h:6,
                   from /tmp/pip-install-gdta70kw/torch-scatter/csrc/cpu/scatter_cpu.h:3,
                   from /tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.cpp:4:
  /usr/lib/python3/dist-packages/torch/include/torch/csrc/utils/pybind.h:6:10: fatal error: pybind11/pybind11.h: No such file or directory
      6 | #include <pybind11/pybind11.h>
        |          ^~~~~~~~~~~~~~~~~~~~~
  compilation terminated.
  error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for torch-scatter
  Running setup.py clean for torch-scatter
Failed to build torch-scatter
ERROR: torch-points3d 1.1.1 requires torch-cluster<1.5.6, which is not installed.
ERROR: torch-points3d 1.1.1 requires torch-points-kernels<0.7.0,>=0.6.6, which is not installed.
ERROR: torch-points3d 1.1.1 requires torch-sparse<0.7.0,>=0.6.0, which is not installed.
Installing collected packages: torch-scatter
    Running setup.py install for torch-scatter ... error
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdta70kw/torch-scatter/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdta70kw/torch-scatter/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-lnvogx36/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/alberto/.local/include/python3.8/torch-scatter
         cwd: /tmp/pip-install-gdta70kw/torch-scatter/
    Complete output (47 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/torch_scatter
    copying torch_scatter/utils.py -> build/lib.linux-x86_64-3.8/torch_scatter
    copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.8/torch_scatter
    copying torch_scatter/scatter.py -> build/lib.linux-x86_64-3.8/torch_scatter
    copying torch_scatter/segment_csr.py -> build/lib.linux-x86_64-3.8/torch_scatter
    copying torch_scatter/placeholder.py -> build/lib.linux-x86_64-3.8/torch_scatter
    copying torch_scatter/segment_coo.py -> build/lib.linux-x86_64-3.8/torch_scatter
    creating build/lib.linux-x86_64-3.8/torch_scatter/composite
    copying torch_scatter/composite/logsumexp.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
    copying torch_scatter/composite/std.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
    copying torch_scatter/composite/__init__.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
    copying torch_scatter/composite/softmax.py -> build/lib.linux-x86_64-3.8/torch_scatter/composite
    running build_ext
    building 'torch_scatter._scatter' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/tmp
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc/cpu
    creating build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc/cuda
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DWITH_CUDA -I/tmp/pip-install-gdta70kw/torch-scatter/csrc -I/usr/lib/python3/dist-packages/torch/include -I/usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include -I/usr/lib/python3/dist-packages/torch/include/TH -I/usr/lib/python3/dist-packages/torch/include/THC -I/usr/include/python3.8 -c /tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.cpp -o build/temp.linux-x86_64-3.8/tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.o -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=_scatter -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++14
    In file included from /usr/lib/python3/dist-packages/torch/include/ATen/Parallel.h:149,
                     from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/utils.h:3,
                     from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/nn/cloneable.h:5,
                     from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/nn.h:3,
                     from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/all.h:7,
                     from /usr/lib/python3/dist-packages/torch/include/torch/extension.h:4,
                     from /tmp/pip-install-gdta70kw/torch-scatter/csrc/cpu/scatter_cpu.h:3,
                     from /tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.cpp:4:
    /usr/lib/python3/dist-packages/torch/include/ATen/ParallelOpenMP.h:84: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       84 | #pragma omp parallel for if ((end - begin) >= grain_size)
          |
    In file included from /usr/lib/python3/dist-packages/torch/include/torch/csrc/api/include/torch/python.h:12,
                     from /usr/lib/python3/dist-packages/torch/include/torch/extension.h:6,
                     from /tmp/pip-install-gdta70kw/torch-scatter/csrc/cpu/scatter_cpu.h:3,
                     from /tmp/pip-install-gdta70kw/torch-scatter/csrc/scatter.cpp:4:
    /usr/lib/python3/dist-packages/torch/include/torch/csrc/utils/pybind.h:6:10: fatal error: pybind11/pybind11.h: No such file or directory
        6 | #include <pybind11/pybind11.h>
          |          ^~~~~~~~~~~~~~~~~~~~~
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-gdta70kw/torch-scatter/setup.py'"'"'; __file__='"'"'/tmp/pip-install-gdta70kw/torch-scatter/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-lnvogx36/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/alberto/.local/include/python3.8/torch-scatter Check the logs for full command output.

Note: you may need to restart the kernel to use updated packages.

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:6 (3 by maintainers)

github_iconTop GitHub Comments

1reaction
rusty1scommented, Oct 30, 2020

I always thought pybind11 comes with PyTorch as there is no need to install it manually in general. I have no idea why it was missing in your case.

Regarding the version: What happens if you run

pip uninstall torch-scatter
pip install torch-scatter==1.3.1
1reaction
rusty1scommented, Oct 29, 2020

You can try to install pybind11:

pip install pybind11
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