Problem when installing torch-scatter

📚 Installation

Environment

• OS:Ubuntu 18.04
• Python version: python 3.7.3
• PyTorch version:1.1.0
• CUDA/cuDNN version: CUDA version 10.0.130
• GCC version:
• How you tried to install PyTorch Geometric and its extensions (pip, source):
• Any other relevant information:

Checklist

• [v ] I followed the installation guide.
• [v ] I cannot find my error message in the FAQ.
• [v ] I set up CUDA correctly and can compile CUDA code via nvcc.
• [v ] I have cloned the repository and tried a manual installation from source.
• [v ] I do have multiple CUDA versions on my machine.
• [v ] I checked if the official extension example runs on my machine.
• [v ] The offical extension example runs on my machine.

Additional context

I tried to install torch-scatter in my virtual environment(pipenv) but it didn’t work.

The specification of my local machine is below. nvcc -version nvcc: NVIDIA ® Cuda compiler driver Copyright © 2005-2018 NVIDIA Corporation Built on Sat_Aug_25_21:08:01_CDT_2018 Cuda compilation tools, release 10.0, V10.0.130

gcc --version gcc (Ubuntu 7.3.0-27ubuntu1~18.04) 7.3.0 Copyright © 2017 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

cat /usr/local/cuda/version.txt CUDA Version 10.0.130

cat /usr/local/cuda/include/cudnn.h | grep CUDNN_MAJOR -A 2 #define CUDNN_MAJOR 7 #define CUDNN_MINOR 5 #define CUDNN_PATCHLEVEL 0

#define CUDNN_VERSION (CUDNN_MAJOR * 1000 + CUDNN_MINOR * 100 + CUDNN_PATCHLEVEL)

#include “driver_types.h”

Then, pipenv install torch-scatter

Output is: ✔ Installation Succeeded Installing dependencies from Pipfile… An error occurred while installing torch-scatter! Will try again. An error occurred while installing torch-sparse! Will try again. An error occurred while installing torch-cluster! Will try again. An error occurred while installing torch-spline-conv! Will try again. 🐍 ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 10/10 — 00:00:05 Installing initially failed dependencies… ☤ ▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉▉ 4/4 — 00:00:15 [pipenv.exceptions.InstallError]: File “/home/sshospital/.local/lib/python3.6/site-packages/pipenv/cli/command.py”, line 254, in install [pipenv.exceptions.InstallError]: editable_packages=state.installstate.editables, [pipenv.exceptions.InstallError]: File “/home/sshospital/.local/lib/python3.6/site-packages/pipenv/core.py”, line 1992, in do_install [pipenv.exceptions.InstallError]: skip_lock=skip_lock, [pipenv.exceptions.InstallError]: File “/home/sshospital/.local/lib/python3.6/site-packages/pipenv/core.py”, line 1253, in do_init [pipenv.exceptions.InstallError]: pypi_mirror=pypi_mirror, [pipenv.exceptions.InstallError]: File “/home/sshospital/.local/lib/python3.6/site-packages/pipenv/core.py”, line 862, in do_install_dependencies [pipenv.exceptions.InstallError]: _cleanup_procs(procs, False, failed_deps_queue, retry=False) [pipenv.exceptions.InstallError]: File “/home/sshospital/.local/lib/python3.6/site-packages/pipenv/core.py”, line 681, in _cleanup_procs [pipenv.exceptions.InstallError]: raise exceptions.InstallError(c.dep.name, extra=err_lines) [pipenv.exceptions.InstallError]: [‘Collecting torch-scatter’, ’ Using cached https://files.pythonhosted.org/packages/07/c0/f7ac424496f4a3bcb31aa993fba29077a6d42fc2624c66e90b58a566a98e/torch_scatter-1.2.0.tar.gz’, ‘Building wheels for collected packages: torch-scatter’, ’ Building wheel for torch-scatter (setup.py): started’, " Building wheel for torch-scatter (setup.py): finished with status ‘error’“, ’ Running setup.py clean for torch-scatter’, ‘Failed to build torch-scatter’, ‘Installing collected packages: torch-scatter’, ’ Running setup.py install for torch-scatter: started’, " Running setup.py install for torch-scatter: finished with status ‘error’”] [pipenv.exceptions.InstallError]: [‘ERROR: Complete output from command /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/bin/python3.7 -u -c 'import setuptools, tokenize;file='“'”'/tmp/pip-install-a7lhvo86/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-j_367rd1 --python-tag cp37:’, ’ ERROR: running bdist_wheel’, ’ running build’, ’ running build_py’, ’ creating build’, ’ creating build/lib.linux-x86_64-3.7’, ’ creating build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/mul.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/sub.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/min.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/max.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/div.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/mean.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/init.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/add.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/std.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ creating build/lib.linux-x86_64-3.7/test’, ’ copying test/test_multi_gpu.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/test_backward.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/test_std.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/utils.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/init.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/test_forward.py -> build/lib.linux-x86_64-3.7/test’, ’ creating build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ copying torch_scatter/utils/gen.py -> build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ copying torch_scatter/utils/ext.py -> build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ copying torch_scatter/utils/init.py -> build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ warning: build_py: byte-compiling is disabled, skipping.‘, ’ ‘, ’ running build_ext’, " building ‘torch_scatter.scatter_cpu’ extension", ’ creating build/temp.linux-x86_64-3.7’, ’ creating build/temp.linux-x86_64-3.7/cpu’, ’ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fdebug-prefix-map=/build/python3.7-0Cmdei/python3.7-3.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/TH -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/THC -I/usr/include/python3.7m -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/include/python3.7m -c cpu/scatter.cpp -o build/temp.linux-x86_64-3.7/cpu/scatter.o -Wno-unused-variable -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=scatter_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11’, ’ In file included from /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/Device.h:3:0,‘, ’ from /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/python.h:8,’, ’ from /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/extension.h:6,‘, ’ from cpu/scatter.cpp:1:’, ’ /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/python_headers.h:9:10: fatal error: Python.h: No such file or directory’, ’ #include <Python.h>‘, ’ ^~‘, ’ compilation terminated.’, " error: command ‘x86_64-linux-gnu-gcc’ failed with exit status 1", ’ ----------------------------------------‘, ’ ERROR: Failed building wheel for torch-scatter’, ’ ERROR: Complete output from command /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/bin/python3.7 -u -c 'import setuptools, tokenize;file='“'”'/tmp/pip-install-a7lhvo86/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-pf6t3kzs/install-record.txt --single-version-externally-managed --compile --install-headers /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/include/site/python3.7/torch-scatter:‘, ’ ERROR: running install’, ’ running build’, ’ running build_py’, ’ creating build’, ’ creating build/lib.linux-x86_64-3.7’, ’ creating build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/mul.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/sub.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/min.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/max.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/div.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/mean.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/init.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/add.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ copying torch_scatter/std.py -> build/lib.linux-x86_64-3.7/torch_scatter’, ’ creating build/lib.linux-x86_64-3.7/test’, ’ copying test/test_multi_gpu.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/test_backward.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/test_std.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/utils.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/init.py -> build/lib.linux-x86_64-3.7/test’, ’ copying test/test_forward.py -> build/lib.linux-x86_64-3.7/test’, ’ creating build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ copying torch_scatter/utils/gen.py -> build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ copying torch_scatter/utils/ext.py -> build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ copying torch_scatter/utils/init.py -> build/lib.linux-x86_64-3.7/torch_scatter/utils’, ’ warning: build_py: byte-compiling is disabled, skipping.‘, ’ ‘, ’ running build_ext’, " building ‘torch_scatter.scatter_cpu’ extension", ’ creating build/temp.linux-x86_64-3.7’, ’ creating build/temp.linux-x86_64-3.7/cpu’, ’ x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -fdebug-prefix-map=/build/python3.7-0Cmdei/python3.7-3.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/api/include -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/TH -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/THC -I/usr/include/python3.7m -I/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/include/python3.7m -c cpu/scatter.cpp -o build/temp.linux-x86_64-3.7/cpu/scatter.o -Wno-unused-variable -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=scatter_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11’, ’ In file included from /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/Device.h:3:0,‘, ’ from /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/api/include/torch/python.h:8,’, ’ from /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/extension.h:6,‘, ’ from cpu/scatter.cpp:1:’, ’ /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/lib/python3.7/site-packages/torch/include/torch/csrc/python_headers.h:9:10: fatal error: Python.h: No such file or directory’, ’ #include <Python.h>', ’ ^~’, ’ compilation terminated.‘, " error: command ‘x86_64-linux-gnu-gcc’ failed with exit status 1", ’ ----------------------------------------’, ‘ERROR: Command “/home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/bin/python3.7 -u -c 'import setuptools, tokenize;file='”'“'/tmp/pip-install-a7lhvo86/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-pf6t3kzs/install-record.txt --single-version-externally-managed --compile --install-headers /home/sshospital/.local/share/virtualenvs/gnn-solve-jssp-YSXwIMg8/include/site/python3.7/torch-scatter” failed with error code 1 in /tmp/pip-install-a7lhvo86/torch-scatter/’]

Could you give me any suggestions?

[michaelzxu]

Stumbled upon this, hope this helps: https://stackoverflow.com/questions/21530577/fatal-error-python-h-no-such-file-or-directory

[jaehyeongchun]

Thanks, I should have installed python3.7-dev!! Now it works well.