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faysalhossain2007 opened this issue Apr 21, 2022 · 6 comments
Closed

Program halts whenever trying to import ogb.graphproppred #39

faysalhossain2007 opened this issue Apr 21, 2022 · 6 comments

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@faysalhossain2007
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Hi I am able to run from torch_geometric.data import InMemoryDataset successfully. But whenever I try to import anything from ogb, the program stuck for infinite time. Import code is: from ogb.graphproppred import Evaluator

I followed the following command to install torch in conda environment:

CUDA=cu113
TORCH=1.11.0
pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
pip install torch-cluster -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
pip install torch-spline-conv -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
pip install torch-geometric
Note that, I am using Ubuntu. My Nvidia-smi output:

$ nvidia-smi
Wed Apr 20 05:09:04 2022
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 450.119.03 Driver Version: 450.119.03 CUDA Version: 11.0 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 GeForce GTX 1070 Off | 00000000:01:00.0 On | N/A |
| 27% 36C P8 9W / 151W | 1227MiB / 8116MiB | 1% Default |
| | | N/A
@vthost
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vthost commented Apr 21, 2022

Hi!
I heard of this problem when using python=3.8 recently. Could you try to change to python=3.9? Also, pytorch geometric is now available on conda. If the python change does not solve the problem, you could try installing it that way: https://pytorch-geometric.readthedocs.io/en/latest/notes/installation.html

@faysalhossain2007
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can you tell me which version of the packages worked for you?
Currently these are the packages that I installed in the conda environment:

conda list
# packages in environment at /home/faysal/anaconda3/envs/pyg:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             4.5                       1_gnu  
blas                      1.0                         mkl  
boost                     1.74.0           py38hc10631b_3    conda-forge
boost-cpp                 1.74.0               h9359b55_0    conda-forge
bottleneck                1.3.4            py38hce1f21e_0  
brotlipy                  0.7.0           py38h27cfd23_1003  
bzip2                     1.0.8                h7b6447c_0  
ca-certificates           2020.10.14                    0    anaconda
cairo                     1.16.0               hf32fb01_1  
certifi                   2021.10.8        py38h06a4308_2  
cffi                      1.15.0           py38hd667e15_1  
charset-normalizer        2.0.4              pyhd3eb1b0_0  
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
cryptography              36.0.0           py38h9ce1e76_0  
cudatoolkit               11.3.1               h2bc3f7f_2  
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
decorator                 4.4.2                      py_0    anaconda
dgl                       0.8.1                    py38_0    dglteam
ffmpeg                    4.3                  hf484d3e_0    pytorch
fontconfig                2.13.1               h6c09931_0  
freetype                  2.11.0               h70c0345_0  
giflib                    5.2.1                h7b6447c_0  
glib                      2.69.1               h4ff587b_1  
gmp                       6.2.1                h2531618_2  
gnutls                    3.6.15               he1e5248_0  
greenlet                  1.1.1            py38h295c915_0  
icu                       67.1                 he1b5a44_0    conda-forge
idna                      3.3                pyhd3eb1b0_0  
intel-openmp              2021.4.0          h06a4308_3561  
jinja2                    3.1.1                    pypi_0    pypi
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9d                   h7f8727e_0  
kiwisolver                1.3.2            py38h295c915_0  
lame                      3.100                h7b6447c_0  
lcms2                     2.12                 h3be6417_0  
ld_impl_linux-64          2.35.1               h7274673_9  
libffi                    3.3                  he6710b0_2  
libgcc-ng                 9.3.0               h5101ec6_17  
libgfortran-ng            7.5.0               ha8ba4b0_17  
libgfortran4              7.5.0               ha8ba4b0_17  
libgomp                   9.3.0               h5101ec6_17  
libiconv                  1.15                 h63c8f33_5  
libidn2                   2.3.2                h7f8727e_0  
libpng                    1.6.37               hbc83047_0  
libstdcxx-ng              9.3.0               hd4cf53a_17  
libtasn1                  4.16.0               h27cfd23_0  
libtiff                   4.2.0                h85742a9_0  
libunistring              0.9.10               h27cfd23_0  
libuuid                   1.0.3                h7f8727e_2  
libuv                     1.40.0               h7b6447c_0  
libwebp                   1.2.2                h55f646e_0  
libwebp-base              1.2.2                h7f8727e_0  
libxcb                    1.14                 h7b6447c_0  
libxml2                   2.9.10               h72b56ed_2    conda-forge
littleutils               0.2.2                      py_0    conda-forge
lz4-c                     1.9.3                h295c915_1  
markupsafe                2.1.1                    pypi_0    pypi
matplotlib-base           3.3.4            py38h0efea84_0    conda-forge
mkl                       2021.4.0           h06a4308_640  
mkl-service               2.4.0            py38h7f8727e_0  
mkl_fft                   1.3.1            py38hd3c417c_0  
mkl_random                1.2.2            py38h51133e4_0  
ncurses                   6.3                  h7f8727e_2  
nettle                    3.7.3                hbbd107a_1  
networkx                  2.5                        py_0    anaconda
numexpr                   2.8.1            py38h6abb31d_0  
numpy                     1.21.5           py38he7a7128_1  
numpy-base                1.21.5           py38hf524024_1  
ogb                       1.3.3                    pypi_0    pypi
openh264                  2.1.1                h4ff587b_0  
openssl                   1.1.1n               h7f8727e_0  
outdated                  0.2.1                    pypi_0    pypi
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.2                    pypi_0    pypi
pcre                      8.45                 h9c3ff4c_0    conda-forge
pillow                    9.0.1            py38h22f2fdc_0  
pip                       21.2.4           py38h06a4308_0  
pixman                    0.40.0               h36c2ea0_0    conda-forge
pycairo                   1.19.1           py38h708ec4a_0  
pycparser                 2.21               pyhd3eb1b0_0  
pyopenssl                 22.0.0             pyhd3eb1b0_0  
pyparsing                 3.0.8              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1            py38h06a4308_0  
python                    3.8.13               h12debd9_0  
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      2_cp38    conda-forge
pytorch                   1.11.0          py3.8_cuda11.3_cudnn8.2.0_0    pytorch
pytorch-mutex             1.0                        cuda    pytorch
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
rdkit                     2020.09.5        py38h2bca085_0    conda-forge
readline                  8.1.2                h7f8727e_1  
reportlab                 3.5.68           py38hadf75a6_0    conda-forge
requests                  2.27.1             pyhd3eb1b0_0  
scikit-learn              1.0.2            py38h51133e4_1  
scipy                     1.8.0                    pypi_0    pypi
setuptools                61.2.0           py38h06a4308_0  
six                       1.16.0             pyhd3eb1b0_1  
sqlalchemy                1.4.13           py38h497a2fe_0    conda-forge
sqlite                    3.38.2               hc218d9a_0  
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tk                        8.6.11               h1ccaba5_0  
torch-cluster             1.6.0                    pypi_0    pypi
torch-geometric           2.0.4                    pypi_0    pypi
torch-scatter             2.0.9                    pypi_0    pypi
torch-sparse              0.6.13                   pypi_0    pypi
torch-spline-conv         1.2.1                    pypi_0    pypi
torchaudio                0.11.0               py38_cu113    pytorch
torchvision               0.12.0               py38_cu113    pytorch
tornado                   6.1              py38h497a2fe_1    conda-forge
tqdm                      4.64.0             pyhd8ed1ab_0    conda-forge
typing_extensions         4.1.1              pyh06a4308_0  
urllib3                   1.26.8             pyhd3eb1b0_0  
wheel                     0.37.1             pyhd3eb1b0_0  
xz                        5.2.5                h7b6447c_0  
zlib                      1.2.12               h7f8727e_1  
zstd                      1.4.9                haebb681_0

@faysalhossain2007
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faysalhossain2007 commented Apr 22, 2022 •
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I installed python 3.9 along with pytorch and torchvision as follow-

conda create --name=pyg9 python=3.9
conda activate pyg9
conda install pyg -c pyg
conda install torchvision
conda install ogb

but it is still having the same issue.

note that while running the code for the first time, I experience the following error:

ImportError: cannot import name 'container_abcs' from 'torch._six' (/home/faysal/anaconda3/envs/pyg9/lib/python3.9/site-packages/torch/_six.py)

I changed it to import collections.abc as container_abcs (according to http://github.com/NVIDIA/apex/issues/1048)

@vthost
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vthost commented Apr 22, 2022 •
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We used these versions for development. It is definitely a good idea to first try with those!

Generally, this seems to be a PyG / PyTorch issue... I am sorry but I am afraid that we are not the right source for support. I would assume you get it running with the versions we used. Otherwise, I would suggest that you open an issue on the PyG GitHub.

@faysalhossain2007
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Thanks for the help! At last I am able to run the code with small dataset with a few modification to the code.

@faysalhossain2007
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faysalhossain2007 commented Apr 22, 2022 •
edited
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Thought of other might get help so posting here my detailed approach:

conda create --name=pyg9 python=3.9
conda activate pyg9
conda install pyg -c pyg
conda install torchvision
conda install ogb

In main.py => I move from ogb.graphproppred import Evaluator to the beginning of the file

In src/data/dataloader.py =>

import torch
from torch.utils.data.dataloader import default_collate
from torch_geometric.data import Data, Batch
from torch._six import  string_classes
import collections.abc as container_abcs

In Line 44: I applied the following modifications:

elif isinstance(elem, int_classes): changed to elif isinstance(elem, int):

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