Pytorch_geometric: Segmentation Fault

[chituma110]

I have run the six scripts in the examples folder. The arma.py, rgcn.py, sgc.py ere fine, however the cora.py, gat.py and gat.py were failed.

Error:
Segmentation fault (core dumped)

System:
python ==3.6.3
pytorch == 1.0.1.post2
torch-geometric == 1.0.3

ubuntu 14.04,
CUDA=8.0
cudnn=7.1.3

[rusty1s]

Can you run the test suite of torch-scatter?

[chituma110]

Thank you for your reply:
I have run the following test code of torch-scatter:

input:

from torch_scatter import scatter_max
import torch
src = torch.tensor([[2,0,1,4,3],[0,2,1,3,4]])
index = torch.tensor([[4,5,4,2,3],[0,0,2,2,1]])
out, argmax = scatter_max(src, index)

output:
Segmentation fault (core dumped)

How can I solve the problem?

[rusty1s]

Can you show me the output of a clean torch-scatter installation?

rm -rf build/ && python setup.py install

[chituma110]

running install
running bdist_egg
running egg_info
writing torch_scatter.egg-info/PKG-INFO
writing dependency_links to torch_scatter.egg-info/dependency_links.txt
writing top-level names to torch_scatter.egg-info/top_level.txt
reading manifest file 'torch_scatter.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'torch_scatter.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/test
copying test/__init__.py -> build/lib.linux-x86_64-3.6/test
copying test/test_backward.py -> build/lib.linux-x86_64-3.6/test
copying test/test_forward.py -> build/lib.linux-x86_64-3.6/test
copying test/test_multi_gpu.py -> build/lib.linux-x86_64-3.6/test
copying test/test_std.py -> build/lib.linux-x86_64-3.6/test
copying test/utils.py -> build/lib.linux-x86_64-3.6/test
creating build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/__init__.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/add.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/div.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/max.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/mean.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/min.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/mul.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/std.py -> build/lib.linux-x86_64-3.6/torch_scatter
copying torch_scatter/sub.py -> build/lib.linux-x86_64-3.6/torch_scatter
creating build/lib.linux-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/__init__.py -> build/lib.linux-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/ext.py -> build/lib.linux-x86_64-3.6/torch_scatter/utils
copying torch_scatter/utils/gen.py -> build/lib.linux-x86_64-3.6/torch_scatter/utils
running build_ext
building 'torch_scatter.scatter_cpu' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/cpu
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/torch/csrc/api/include -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/TH -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/THC -I/home/amax/anaconda2/envs/pytorch10_python3/include/python3.6m -c cpu/scatter.cpp -o build/temp.linux-x86_64-3.6/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
cc1plus: warning: command line option \u2018-Wstrict-prototypes\u2019 is valid for C/ObjC but not for C++
g++ -pthread -shared -L/home/amax/anaconda2/envs/pytorch10_python3/lib -Wl,-rpath=/home/amax/anaconda2/envs/pytorch10_python3/lib,--no-as-needed -L/home/amax/anaconda2/envs/pytorch10_python3/lib -Wl,-rpath=/home/amax/anaconda2/envs/pytorch10_python3/lib,--no-as-needed build/temp.linux-x86_64-3.6/cpu/scatter.o -L/home/amax/anaconda2/envs/pytorch10_python3/lib -lpython3.6m -o build/lib.linux-x86_64-3.6/torch_scatter/scatter_cpu.cpython-36m-x86_64-linux-gnu.so
building 'torch_scatter.scatter_cuda' extension
creating build/temp.linux-x86_64-3.6/cuda
gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/torch/csrc/api/include -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/TH -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/THC -I/usr/local/cuda/include -I/home/amax/anaconda2/envs/pytorch10_python3/include/python3.6m -c cuda/scatter.cpp -o build/temp.linux-x86_64-3.6/cuda/scatter.o -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=scatter_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
cc1plus: warning: command line option \u2018-Wstrict-prototypes\u2019 is valid for C/ObjC but not for C++
/usr/local/cuda/bin/nvcc -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/torch/csrc/api/include -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/TH -I/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch/lib/include/THC -I/usr/local/cuda/include -I/home/amax/anaconda2/envs/pytorch10_python3/include/python3.6m -c cuda/scatter_kernel.cu -o build/temp.linux-x86_64-3.6/cuda/scatter_kernel.o -D__CUDA_NO_HALF_OPERATORS__ -D__CUDA_NO_HALF_CONVERSIONS__ -D__CUDA_NO_HALF2_OPERATORS__ --compiler-options '-fPIC' -DTORCH_API_INCLUDE_EXTENSION_H -DTORCH_EXTENSION_NAME=scatter_cuda -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning).
g++ -pthread -shared -L/home/amax/anaconda2/envs/pytorch10_python3/lib -Wl,-rpath=/home/amax/anaconda2/envs/pytorch10_python3/lib,--no-as-needed -L/home/amax/anaconda2/envs/pytorch10_python3/lib -Wl,-rpath=/home/amax/anaconda2/envs/pytorch10_python3/lib,--no-as-needed build/temp.linux-x86_64-3.6/cuda/scatter.o build/temp.linux-x86_64-3.6/cuda/scatter_kernel.o -L/usr/local/cuda/lib64 -L/home/amax/anaconda2/envs/pytorch10_python3/lib -lcudart -lpython3.6m -o build/lib.linux-x86_64-3.6/torch_scatter/scatter_cuda.cpython-36m-x86_64-linux-gnu.so
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/test
copying build/lib.linux-x86_64-3.6/test/__init__.py -> build/bdist.linux-x86_64/egg/test
copying build/lib.linux-x86_64-3.6/test/test_backward.py -> build/bdist.linux-x86_64/egg/test
copying build/lib.linux-x86_64-3.6/test/test_forward.py -> build/bdist.linux-x86_64/egg/test
copying build/lib.linux-x86_64-3.6/test/test_multi_gpu.py -> build/bdist.linux-x86_64/egg/test
copying build/lib.linux-x86_64-3.6/test/test_std.py -> build/bdist.linux-x86_64/egg/test
copying build/lib.linux-x86_64-3.6/test/utils.py -> build/bdist.linux-x86_64/egg/test
creating build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/__init__.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/add.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/div.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/max.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/mean.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/min.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/mul.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/scatter_cpu.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/scatter_cuda.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/std.py -> build/bdist.linux-x86_64/egg/torch_scatter
copying build/lib.linux-x86_64-3.6/torch_scatter/sub.py -> build/bdist.linux-x86_64/egg/torch_scatter
creating build/bdist.linux-x86_64/egg/torch_scatter/utils
copying build/lib.linux-x86_64-3.6/torch_scatter/utils/__init__.py -> build/bdist.linux-x86_64/egg/torch_scatter/utils
copying build/lib.linux-x86_64-3.6/torch_scatter/utils/ext.py -> build/bdist.linux-x86_64/egg/torch_scatter/utils
copying build/lib.linux-x86_64-3.6/torch_scatter/utils/gen.py -> build/bdist.linux-x86_64/egg/torch_scatter/utils
byte-compiling build/bdist.linux-x86_64/egg/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/test/test_backward.py to test_backward.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/test/test_forward.py to test_forward.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/test/test_multi_gpu.py to test_multi_gpu.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/test/test_std.py to test_std.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/test/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/add.py to add.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/div.py to div.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/max.py to max.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/mean.py to mean.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/min.py to min.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/mul.py to mul.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/std.py to std.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/sub.py to sub.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/utils/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/utils/ext.py to ext.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/utils/gen.py to gen.cpython-36.pyc
creating stub loader for torch_scatter/scatter_cpu.cpython-36m-x86_64-linux-gnu.so
creating stub loader for torch_scatter/scatter_cuda.cpython-36m-x86_64-linux-gnu.so
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/scatter_cpu.py to scatter_cpu.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/torch_scatter/scatter_cuda.py to scatter_cuda.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying torch_scatter.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying torch_scatter.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying torch_scatter.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying torch_scatter.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
torch_scatter.__pycache__.scatter_cpu.cpython-36: module references __file__
torch_scatter.__pycache__.scatter_cuda.cpython-36: module references __file__
creating 'dist/torch_scatter-1.1.2-py3.6-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing torch_scatter-1.1.2-py3.6-linux-x86_64.egg
removing '/home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch_scatter-1.1.2-py3.6-linux-x86_64.egg' (and everything under it)
creating /home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch_scatter-1.1.2-py3.6-linux-x86_64.egg
Extracting torch_scatter-1.1.2-py3.6-linux-x86_64.egg to /home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages
torch-scatter 1.1.2 is already the active version in easy-install.pth

Installed /home/amax/anaconda2/envs/pytorch10_python3/lib/python3.6/site-packages/torch_scatter-1.1.2-py3.6-linux-x86_64.egg
Processing dependencies for torch-scatter==1.1.2
Finished processing dependencies for torch-scatter==1.1.2

[rusty1s]

I created a FAQ for common installation errors. Let me know if this fixes your issues.

[jzhou316]

I ran into the same error "Segmentation fault (core dumped)" for some of the examples.

[ez4lionky]

The error "Segmentation fault" occurred for gat.py

[weitianxin]

I ran into the same error, some examples worked fine and some not. I also tried to re-install the torch-scatter module but also got Segmentation Fault. How can I solve this problem?

[dblakely]

I believe all of the segfaults are caused by building with an older version of gcc. I'm using a conda environment and did conda install gcc_linux-64 gxx_linux-64 and reinstalled pytorch and each of pytorch geometric libraries.

[jzhou316]

I found the "Segmentation Fault" happens in particular with scatter_max function. That's why gat.py, etc. failed.

[dragen1860]

Hi, I met this error while my server gcc version is : 4.8.5. When i update it using conda install -c omgarcia gcc-6 and just re-install torch-scatter, torch-sparse, torch-cluster, torch-geometric only, everything goes well.

[ChandlerBang]

I believe all of the segfaults are caused by building with an older version of gcc. I'm using a conda environment and did conda install gcc_linux-64 gxx_linux-64 and reinstalled pytorch and each of pytorch geometric libraries.

Thanks a lot! This really helps.

[yrf1]

After doing conda install gcc_linux-64 gxx_linux-64 the gcc is not found, can some tell me how can i activate the gcc installed?

[rusty1s]

You can try CC=... CXX=... pip install torch-scatter to explicitly set your path to gcc.

[prokia]

After doing conda install gcc_linux-64 gxx_linux-64 the gcc is not found, can some tell me how can i activate the gcc installed?

I ran into the same error, how did you fix it?