A small question about seal

[muhanzhang]

你好。util 文件来自pytorch_DGCNN，需要在使用SEAL前提前下载安装到跟SEAL相同level的文件夹下。你可以执行“bash ./install.sh” 来自动安装pytorch_DGCNN 以及其他所需要的包。谢谢！

[QiAyo523]

好的，非常感谢哦！我也在您的其他项目里面找到这个了，😃 (^m^ )------------------ 原始邮件 ------------------ 发件人: "Muhan Zhang"<[email protected]> 发送时间: 2019年8月22日(星期四) 晚上11:34 收件人: "muhanzhang/SEAL"<[email protected]>; 抄送: "QiAyo523"<[email protected]>;"Author"<[email protected]>; 主题: Re: [muhanzhang/SEAL] A small question (#20) 你好。util 文&#x4EF6;来自pytorch_DGCNN，需要在使用SEAL前提前下载安装到跟SEAL相同level的文&#x4EF6;夹下。你可以执行“bash ./install.sh” 来自动安装pytorch_DGCNN 以及其他所需要的包。谢谢！ &mdash; You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[QiAyo523]

你好，我在mac上运行Main.py时，有io异常，具体是OSError: dlopen(/Users/lijuan/PythonCode/pytorch_DGCNN/lib/build/dll/libgnn.so, 6): no suitable image found. Did find:，我尝试了网上的解决方案，都不能解决，请问你是否遇到过这样的问题呢？

[muhanzhang]

Hi, please check out this issue: #17

[QiAyo523]

Thank you very much！------------------ 原始邮件 ------------------ 发件人: "Muhan Zhang"<[email protected]> 发送时间: 2019年8月26日(星期一) 凌晨2:48 收件人: "muhanzhang/SEAL"<[email protected]>; 抄送: "QiAyo523"<[email protected]>;"Author"<[email protected]>; 主题: Re: [muhanzhang/SEAL] A small question (#20) Hi, please check out this issue: #17 &mdash; You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[QiAyo523]

Sorry，I get a new error when I run this code, and I think the written is correct，but I can't find the reason. Maybe the data is not load?
Traceback (most recent call last):
File "Main.py", line 103, in
train_graphs, test_graphs, max_n_label = links2subgraphs(A, train_pos, train_neg, test_pos, test_neg, args.hop, args.max_nodes_per_hop, node_information)
File "/home/wangwang/SEAL-master/Python/util_functions.py", line 106, in links2subgraphs
train_graphs = helper(A, train_pos, 1) + helper(A, train_neg, 0)
File "/home/wangwang/SEAL-master/Python/util_functions.py", line 99, in helper
g_list = [GNNGraph(g, g_label, n_labels, n_features) for g, n_labels, n_features in results]
File "/home/wangwang/SEAL-master/Python/../../pytorch_DGCNN/util.py", line 53, in init
self.degs = list(dict(g.degree).values())
TypeError: 'instancemethod' object is not iterable

[muhanzhang]

Which networkx version did you use? Sometimes try to replace "g.degree" with "g.degree()" solves this issue.

[QiAyo523]

That's OK! Thanks!
The networkx version on the server is too low. ==||

[QiAyo523]

Hello, dose your model output the probability of a link between the nodepairs?

[muhanzhang]

Hi, please check out this issue: #10

And please try to first look for your question in existing issues. Many of them have been answered before. Thanks!

[QiAyo523]

Oh, I see, thank you, and I'm sorry to have caused so much trouble to you. 😂------------------ 原始邮件 ------------------ 发件人: "Muhan Zhang"<[email protected]> 发送时间: 2019年8月30日(星期五) 凌晨0:20 收件人: "muhanzhang/SEAL"<[email protected]>; 抄送: "QiAyo523"<[email protected]>;"Author"<[email protected]>; 主题: Re: [muhanzhang/SEAL] A small question (#20) Hi, please check out this issue: #10 And please try to first look for your question in existing issues. Many of them have been answered before. Thanks! &mdash; You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[xihairanfeng]

您好，我在服务器上跑的时候也遇到了相同的问题。然后进行了下面的步骤（bash ./install.sh）
(base) czw@sy-NF5280M5:~/seal/SEAL/Python$ bash ./install.sh
结果出现了
./install.sh: line 2: $'\r': command not found
./install.sh: line 3: cd: $'../../\r': No such file or directory
fatal: destination path 'pytorch_DGCNN' already exists and is not an empty directory.
./install.sh: line 5: cd: $'pytorch_DGCNN\r': No such file or directory
./install.sh: line 6: cd: $'lib\r': No such file or directory
make: the '-j' option requires a positive integer argument
Usage: make [options] [target] ...
Options:
-b, -m Ignored for compatibility.
-B, --always-make Unconditionally make all targets.
-C DIRECTORY, --directory=DIRECTORY
Change to DIRECTORY before doing anything.
-d Print lots of debugging information.
--debug[=FLAGS] Print various types of debugging information.
-e, --environment-overrides
Environment variables override makefiles.
--eval=STRING Evaluate STRING as a makefile statement.
-f FILE, --file=FILE, --makefile=FILE
Read FILE as a makefile.
-h, --help Print this message and exit.
-i, --ignore-errors Ignore errors from recipes.
-I DIRECTORY, --include-dir=DIRECTORY
Search DIRECTORY for included makefiles.
-j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg.
-k, --keep-going Keep going when some targets can't be made.
-l [N], --load-average[=N], --max-load[=N]
Don't start multiple jobs unless load is below N.
-L, --check-symlink-times Use the latest mtime between symlinks and target.
-n, --just-print, --dry-run, --recon
Don't actually run any recipe; just print them.
-o FILE, --old-file=FILE, --assume-old=FILE
Consider FILE to be very old and don't remake it.
-O[TYPE], --output-sync[=TYPE]
Synchronize output of parallel jobs by TYPE.
-p, --print-data-base Print make's internal database.
-q, --question Run no recipe; exit status says if up to date.
-r, --no-builtin-rules Disable the built-in implicit rules.
-R, --no-builtin-variables Disable the built-in variable settings.
-s, --silent, --quiet Don't echo recipes.
-S, --no-keep-going, --stop
Turns off -k.
-t, --touch Touch targets instead of remaking them.
--trace Print tracing information.
-v, --version Print the version number of make and exit.
-w, --print-directory Print the current directory.
--no-print-directory Turn off -w, even if it was turned on implicitly.
-W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE
Consider FILE to be infinitely new.
--warn-undefined-variables Warn when an undefined variable is referenced.

This program built for x86_64-pc-linux-gnu
Report bugs to [email protected]
./install.sh: line 8: cd: $'.\r': No such file or directory
Requirement already satisfied: numpy in /home/czw/anaconda3/lib/python3.7/site-packages (1.18.1)
Requirement already satisfied: scipy in /home/czw/anaconda3/lib/python3.7/site-packages (1.4.1)
Requirement already satisfied: numpy>=1.13.3 in /home/czw/anaconda3/lib/python3.7/site-packages (from scipy) (1.18.1)
Requirement already satisfied: networkx in /home/czw/anaconda3/lib/python3.7/site-packages (2.4)
Requirement already satisfied: decorator>=4.3.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from networkx) (4.4.1)
Requirement already satisfied: tqdm in /home/czw/anaconda3/lib/python3.7/site-packages (4.42.1)
Requirement already satisfied: sklearn in /home/czw/.local/lib/python3.7/site-packages (0.0)
Requirement already satisfied: scikit-learn in /home/czw/anaconda3/lib/python3.7/site-packages (from sklearn) (0.22.1)
Requirement already satisfied: numpy>=1.11.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from scikit-learn->sklearn) (1.18.1)
Requirement already satisfied: scipy>=0.17.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from scikit-learn->sklearn) (1.4.1)
Requirement already satisfied: joblib>=0.11 in /home/czw/anaconda3/lib/python3.7/site-packages (from scikit-learn->sklearn) (0.14.1)
Requirement already satisfied: gensim in /home/czw/anaconda3/lib/python3.7/site-packages (3.8.3)
Requirement already satisfied: smart-open>=1.8.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (2.1.0)
Requirement already satisfied: scipy>=0.18.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (1.4.1)
Requirement already satisfied: six>=1.5.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (1.14.0)
Requirement already satisfied: numpy>=1.11.3 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (1.18.1)
Requirement already satisfied: boto in /home/czw/anaconda3/lib/python3.7/site-packages (from smart-open>=1.8.1->gensim) (2.49.0)
Requirement already satisfied: boto3 in /home/czw/anaconda3/lib/python3.7/site-packages (from smart-open>=1.8.1->gensim) (1.14.23)
Requirement already satisfied: requests in /home/czw/anaconda3/lib/python3.7/site-packages (from smart-open>=1.8.1->gensim) (2.22.0)
Requirement already satisfied: botocore<1.18.0,>=1.17.23 in /home/czw/anaconda3/lib/python3.7/site-packages (from boto3->smart-open>=1.8.1->gensim) (1.17.23)
Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from boto3->smart-open>=1.8.1->gensim) (0.10.0)
Requirement already satisfied: s3transfer<0.4.0,>=0.3.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from boto3->smart-open>=1.8.1->gensim) (0.3.3)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (2.8)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (1.25.8)
Requirement already satisfied: certifi>=2017.4.17 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (2019.11.28)
Requirement already satisfied: docutils<0.16,>=0.10 in /home/czw/anaconda3/lib/python3.7/site-packages (from botocore<1.18.0,>=1.17.23->boto3->smart-open>=1.8.1->gensim) (0.15.2)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from botocore<1.18.0,>=1.17.23->boto3->smart-open>=1.8.1->gensim) (2.8.1)
然后后面进行(base) czw@sy-NF5280M5:~/seal/SEAL/Python$ python3 Main.py --data-name NS --test-ratio 0.5 --hop 'auto' --use-embedding
出现的还是这样的问题（）
Traceback (most recent call last):
File "Main.py", line 13, in
from util_functions import *
File "/home/czw/seal/SEAL/Python/util_functions.py", line 17, in
from util import GNNGraph
ModuleNotFoundError: No module named 'util'

也就是我执行了bash ./install.sh，还是出现一样的问题

[xihairanfeng]

您好，我在服务器上跑的时候也遇到了相同的问题。然后进行了下面的步骤（bash ./install.sh）
(base) czw@sy-NF5280M5:~/seal/SEAL/Python$ bash ./install.sh
结果出现了
./install.sh: line 2: $'\r': command not found
./install.sh: line 3: cd: $'../../\r': No such file or directory
fatal: destination path 'pytorch_DGCNN' already exists and is not an empty directory.
./install.sh: line 5: cd: $'pytorch_DGCNN\r': No such file or directory
./install.sh: line 6: cd: $'lib\r': No such file or directory
make: the '-j' option requires a positive integer argument
Usage: make [options] [target] ...
Options:
-b, -m Ignored for compatibility.
-B, --always-make Unconditionally make all targets.
-C DIRECTORY, --directory=DIRECTORY
Change to DIRECTORY before doing anything.
-d Print lots of debugging information.
--debug[=FLAGS] Print various types of debugging information.
-e, --environment-overrides
Environment variables override makefiles.
--eval=STRING Evaluate STRING as a makefile statement.
-f FILE, --file=FILE, --makefile=FILE
Read FILE as a makefile.
-h, --help Print this message and exit.
-i, --ignore-errors Ignore errors from recipes.
-I DIRECTORY, --include-dir=DIRECTORY
Search DIRECTORY for included makefiles.
-j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg.
-k, --keep-going Keep going when some targets can't be made.
-l [N], --load-average[=N], --max-load[=N]
Don't start multiple jobs unless load is below N.
-L, --check-symlink-times Use the latest mtime between symlinks and target.
-n, --just-print, --dry-run, --recon
Don't actually run any recipe; just print them.
-o FILE, --old-file=FILE, --assume-old=FILE
Consider FILE to be very old and don't remake it.
-O[TYPE], --output-sync[=TYPE]
Synchronize output of parallel jobs by TYPE.
-p, --print-data-base Print make's internal database.
-q, --question Run no recipe; exit status says if up to date.
-r, --no-builtin-rules Disable the built-in implicit rules.
-R, --no-builtin-variables Disable the built-in variable settings.
-s, --silent, --quiet Don't echo recipes.
-S, --no-keep-going, --stop
Turns off -k.
-t, --touch Touch targets instead of remaking them.
--trace Print tracing information.
-v, --version Print the version number of make and exit.
-w, --print-directory Print the current directory.
--no-print-directory Turn off -w, even if it was turned on implicitly.
-W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE
Consider FILE to be infinitely new.
--warn-undefined-variables Warn when an undefined variable is referenced.

This program built for x86_64-pc-linux-gnu
Report bugs to [email protected]
./install.sh: line 8: cd: $'.\r': No such file or directory
Requirement already satisfied: numpy in /home/czw/anaconda3/lib/python3.7/site-packages (1.18.1)
Requirement already satisfied: scipy in /home/czw/anaconda3/lib/python3.7/site-packages (1.4.1)
Requirement already satisfied: numpy>=1.13.3 in /home/czw/anaconda3/lib/python3.7/site-packages (from scipy) (1.18.1)
Requirement already satisfied: networkx in /home/czw/anaconda3/lib/python3.7/site-packages (2.4)
Requirement already satisfied: decorator>=4.3.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from networkx) (4.4.1)
Requirement already satisfied: tqdm in /home/czw/anaconda3/lib/python3.7/site-packages (4.42.1)
Requirement already satisfied: sklearn in /home/czw/.local/lib/python3.7/site-packages (0.0)
Requirement already satisfied: scikit-learn in /home/czw/anaconda3/lib/python3.7/site-packages (from sklearn) (0.22.1)
Requirement already satisfied: numpy>=1.11.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from scikit-learn->sklearn) (1.18.1)
Requirement already satisfied: scipy>=0.17.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from scikit-learn->sklearn) (1.4.1)
Requirement already satisfied: joblib>=0.11 in /home/czw/anaconda3/lib/python3.7/site-packages (from scikit-learn->sklearn) (0.14.1)
Requirement already satisfied: gensim in /home/czw/anaconda3/lib/python3.7/site-packages (3.8.3)
Requirement already satisfied: smart-open>=1.8.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (2.1.0)
Requirement already satisfied: scipy>=0.18.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (1.4.1)
Requirement already satisfied: six>=1.5.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (1.14.0)
Requirement already satisfied: numpy>=1.11.3 in /home/czw/anaconda3/lib/python3.7/site-packages (from gensim) (1.18.1)
Requirement already satisfied: boto in /home/czw/anaconda3/lib/python3.7/site-packages (from smart-open>=1.8.1->gensim) (2.49.0)
Requirement already satisfied: boto3 in /home/czw/anaconda3/lib/python3.7/site-packages (from smart-open>=1.8.1->gensim) (1.14.23)
Requirement already satisfied: requests in /home/czw/anaconda3/lib/python3.7/site-packages (from smart-open>=1.8.1->gensim) (2.22.0)
Requirement already satisfied: botocore<1.18.0,>=1.17.23 in /home/czw/anaconda3/lib/python3.7/site-packages (from boto3->smart-open>=1.8.1->gensim) (1.17.23)
Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from boto3->smart-open>=1.8.1->gensim) (0.10.0)
Requirement already satisfied: s3transfer<0.4.0,>=0.3.0 in /home/czw/anaconda3/lib/python3.7/site-packages (from boto3->smart-open>=1.8.1->gensim) (0.3.3)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (2.8)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (1.25.8)
Requirement already satisfied: certifi>=2017.4.17 in /home/czw/anaconda3/lib/python3.7/site-packages (from requests->smart-open>=1.8.1->gensim) (2019.11.28)
Requirement already satisfied: docutils<0.16,>=0.10 in /home/czw/anaconda3/lib/python3.7/site-packages (from botocore<1.18.0,>=1.17.23->boto3->smart-open>=1.8.1->gensim) (0.15.2)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/czw/anaconda3/lib/python3.7/site-packages (from botocore<1.18.0,>=1.17.23->boto3->smart-open>=1.8.1->gensim) (2.8.1)
然后后面进行(base) czw@sy-NF5280M5:~/seal/SEAL/Python$ python3 Main.py --data-name NS --test-ratio 0.5 --hop 'auto' --use-embedding
出现的还是这样的问题（）
Traceback (most recent call last):
File "Main.py", line 13, in
from util_functions import *
File "/home/czw/seal/SEAL/Python/util_functions.py", line 17, in
from util import GNNGraph
ModuleNotFoundError: No module named 'util'

也就是我执行了bash ./install.sh，还是出现一样的问题

我在当前目录执行了install.sh里面的每一步，通过了这个问题（当然cd 到这个是不通过的 dirname $0，自己切换到当前脚本的目录执行的后面的 ）

[muhanzhang]

'\r': command not found

Hi，你是不是有在windows和linux之间拷贝过？可以参考这个https://blog.csdn.net/u010416101/article/details/80135293

[zackzhou0814]

Hello Dr.Zhang. I'm also trying to run the command to install all the packages I need, but I got some errors:

(untitled) C:\Users\84536\PycharmProjects\SEAL\Python>bash ./install.sh
Cloning into 'pytorch_DGCNN'...
remote: Enumerating objects: 453, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 453 (delta 0), reused 2 (delta 0), pack-reused 448
Receiving objects: 100% (453/453), 49.61 MiB | 3.14 MiB/s, done.
Resolving deltas: 100% (96/96), done.
Updating files: 100% (277/277), done.
./install.sh: line 7: make: command not found
./install.sh: line 9: pip: command not found
./install.sh: line 10: pip: command not found
./install.sh: line 11: pip: command not found
./install.sh: line 12: pip: command not found
./install.sh: line 13: pip: command not found
./install.sh: line 14: pip: command not found

I'm running this project on Windows, it seems like the pytorch_DGCNN folder IS at the same level as the root SEAL folder, but I think there still something else is missing since there are a bunch of "commands not found", and when I try to install util package it always fails. It gives this error:
PackagesNotFoundError: The following packages are not available from current channels:
Command output:
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

• util

Current channels:

• https://repo.anaconda.com/pkgs/main/win-64
• https://repo.anaconda.com/pkgs/main/noarch
• https://repo.anaconda.com/pkgs/r/win-64
• https://repo.anaconda.com/pkgs/r/noarch
• https://repo.anaconda.com/pkgs/msys2/win-64
• https://repo.anaconda.com/pkgs/msys2/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Any help would be much appreciated!

[muhanzhang]

Hi, the "install.sh" only runs on linux-based systems. If you run it on windows, you need to manually install the packages. However, I would recommend to directly use the latest SEAL_OGB repository, which uses modern GNN library (pytorch geometric) and supports faster inference speed and large-scale datasets.