benedekrozemberczki / mixhop-and-n-gcn Goto Github PK

hello,How should I construct cora_feature.json? I don't know what the information is. Can you explain it?

I cannot successfully install "torch_scatter".
When I run the command line : pip3 install torch_scatter, an error always occurs, just like below. I tried to solve the problem, but I don't find the correct method. Could you help me? Thanks a lot!

The error:
...
cpu/scatter.cpp:1:29: fatal error: torch/extension.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Failed building wheel for torch-scatter
Running setup.py clean for torch-scatter
Failed to build torch-scatter
Installing collected packages: torch-scatter
Running setup.py install for torch-scatter ... error
Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-ijd9s63n/torch-scatter/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-4tkx7v_s-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/mul.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/mean.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/sub.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/min.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/std.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/init.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/max.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/div.py -> build/lib.linux-x86_64-3.5/torch_scatter
copying torch_scatter/add.py -> build/lib.linux-x86_64-3.5/torch_scatter
creating build/lib.linux-x86_64-3.5/test
copying test/test_multi_gpu.py -> build/lib.linux-x86_64-3.5/test
copying test/utils.py -> build/lib.linux-x86_64-3.5/test
copying test/test_std.py -> build/lib.linux-x86_64-3.5/test
copying test/init.py -> build/lib.linux-x86_64-3.5/test
copying test/test_forward.py -> build/lib.linux-x86_64-3.5/test
copying test/test_backward.py -> build/lib.linux-x86_64-3.5/test
creating build/lib.linux-x86_64-3.5/torch_scatter/utils
copying torch_scatter/utils/ext.py -> build/lib.linux-x86_64-3.5/torch_scatter/utils
copying torch_scatter/utils/init.py -> build/lib.linux-x86_64-3.5/torch_scatter/utils
copying torch_scatter/utils/gen.py -> build/lib.linux-x86_64-3.5/torch_scatter/utils
running build_ext
building 'torch_scatter.scatter_cpu' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/cpu
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/home/zgh/.local/lib/python3.5/site-packages/torch/lib/include -I/home/zgh/.local/lib/python3.5/site-packages/torch/lib/include/TH -I/home/zgh/.local/lib/python3.5/site-packages/torch/lib/include/THC -I/usr/include/python3.5m -c cpu/scatter.cpp -o build/temp.linux-x86_64-3.5/cpu/scatter.o -Wno-unused-variable -DTORCH_EXTENSION_NAME=scatter_cpu -D_GLIBCXX_USE_CXX11_ABI=0 -std=c++11
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
cpu/scatter.cpp:1:29: fatal error: torch/extension.h: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

----------------------------------------

Command "/usr/bin/python3 -u -c "import setuptools, tokenize;file='/tmp/pip-build-ijd9s63n/torch-scatter/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-4tkx7v_s-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-ijd9s63n/torch-scatter/
You are using pip version 8.1.1, however version 19.1.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

To me it looks like this is implementing
H(l+1) = σ(A^j * H(l) * W(l))

Can you explain where W_j and the concatenation are taking place?

hello, when I run main.py, the error message occurs:

File "D:\anaconda3.4\lib\site-packages\torch_sparse\spmm.py", line 30, in spmm
out = matrix[col]
IndexError: index 10241 is out of bounds for dimension 0 with size 10241

the content of the spmm.py:
`# import torch
from torch_scatter import scatter_add

def spmm(index, value, m, n, matrix):
"""Matrix product of sparse matrix with dense matrix.
稀疏矩阵与稠密矩阵的矩阵乘积

Args:
    index (:class:`LongTensor`): The index tensor of sparse matrix.
    value (:class:`Tensor`): The value tensor of sparse matrix.
    m (int): The first dimension of corresponding dense matrix.
    n (int): The second dimension of corresponding dense matrix.
    matrix (:class:`Tensor`): The dense matrix.
  :rtype: :class:`Tensor`
"""

assert n == matrix.size(0)

row, col = index

matrix = matrix if matrix.dim() > 1 else matrix.unsqueeze(-1)

out = matrix[col]
out = out * value.unsqueeze(-1)
out = scatter_add(out, row, dim=0, dim_size=m)

return out

`
by the way, I use my own datasets, and the number of node is 10242. do you know how to solve it?

I didn't find this paper "A Higher-Order Graph Convolutional Layer" in NeuralPS 2018 accepted list.
So I am not sure whether this paper has been accepted?

Can you release the scripts to create input JSON-like files so that we can evaluate it on more datasets?

hello, when I run main.py, the error message occurs:
File "/home/tj/anaconda3/lib/python3.6/site-packages/torch_sparse/init.py", line 22, in
raise OSError(e)
OSError: libcusparse.so.10.0: cannot open shared object file: No such file or directory

my python version 3.6 cuda10.0 torch1.0.1 torch-sparse0.5.1
do you know how to solve it?

hello,
when i run src/main.py，the error message appears:
File "pandas_libs\parsers.pyx", line 361, in pandas._libs.parsers.TextReader.cinit
File "pandas_libs\parsers.pyx", line 653, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] No such file or directory: './input/cora_edges.csv'

do you know how to solve it?

When I run the code, some error occured as follows:
MixHop-and-N-GCN-master\src\utils.py", line 45, in feature_reader out_features["indices"] = torch.LongTensor(np.concatenate([features.row.reshape(-1,1), features.col.reshape(-1,1)],axis=1).T) TypeError: can't convert np.ndarray of type numpy.int32. The only supported types are: float64, float32, float16, int64, int32, int16, int8, and uint8.
I search it on the Internet and found that it seems to be a list of lists that are not of the same length. I was stuck in it and do not know how to correct it! Looking forward to your help!!Thanks!!

Hi Benedek,

Thank you so much for the code. I want to run your code on Citeseer and Pubmed datasets. Would you mind providing Citeseer and Pubmed data in this format? By the way, after running MixHop model with default parameters I got the test accuracy 0.7867. Did the accuracy depend on the system that the code is running?

Thanks in advance

thanks for your well documented repo.
Is this official implementation?